Docking Manual

Docking Suite Manual
SYBYL®-X 2.1
Mid 2013
1699 South Hanley Rd. Phone: +1.314.647.1099

St. Louis, MO Fax: +1.314.647.9241
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following patents: AllChem: US 7,860,657; Comparative Molecular Field Analysis (CoMFA): US 5,025,388; US
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Docking Suite Table of Contents
1. Introduction to the Docking Suite . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

1.1 What is New with the Docking Suite . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
1.2 License Requirements for the Docking Suite . . . . . . . . . . . . . . . . . . . . . . . . . 7
2. Surflex-Dock Tutorial . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
2.1 Perform a Simple Surflex-Dock Run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
2.2 Use Placed Fragments to Guide Docking . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
2.3 Allow Protein Movement to Accommodate Docked Ligands . . . . . . . . . . . . 28
2.4 Validation Study . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
3. Using the Docking Suite . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31

3.1 Prepare and Submit a Docking Job . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
3.2 Analyze Docking Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
4. Surflex-Dock . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
4.1 Run Surflex-Dock Standalone . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
4.2 The Surflex-Dock Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
SYBYL-X 2.1 Docking Suite 3

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1. Introduction to the Docking Suite
SYBYL provides a graphical interface to Surflex-Dock.
Surflex-Dock uses an empirical scoring function and a patented search engine to

dock ligands into a protein’s binding site. Docking is guided by the protomol,
an idealized representation of a ligand that makes every potential interaction
with the binding site. The protomol can be generated automatically or defined
based on a cognate ligand or known active site.
Surflex-Dock is particularly successful at eliminating false positive results and

can, therefore, be used to narrow down the screening pool significantly, while
still retaining a large number of active compounds.
Reading Material
• BioPharmics’ Surflex Manual: Docking and Similarity
• See the list of Recommended Reading about Surflex-Dock on page 80.
Acknowledgments
Surflex-Dock was developed by Prof. Ajay N. Jain, University of California San
Francisco (UCSF) and BioPharmics LLC.

What is New with the Docking Suite
1.1 What is New with the Docking Suite

New Surflex Version
SYBYL-X 2.1 distributes Surflex v.2.706 from BioPharmics IT. Additions and
modifications in this release are highlighted in red in BioPharmics’ Surflex
Manual: Docking and Similarity.
With the changes in Surflex, the Surflex-Dock and Surflex-Dock Screen

modes became identical. As a result, the Surflex-Dock docking mode has been
removed from the list of available docking modes in the main Docking dialog.
SYBYL’s interface to Surflex-Dock includes a new feature to identify the

residues that are allowed to be flexible during a docking run that includes
protein flexibility. This option is accessible in the Surflex-Dock - Details dialog
(Results Optimization section).
New Job Submission Options

The Netbatch Options section of the Docking dialog has been replaced with a
new Job Submission section, which now provides easy access to the various
job execution choices available for docking jobs (e.g., interactive, local, remote,
multiple machines, multiple processors and grids).
Multiple Engines
Running Surflex-Dock with one fragment selected and specifying more than
one engine would fail in SYBYL-X 2.0. This issue no longer occurs.
Defining Protomol by Residues

An issue that prevented setting up a protomol using protein residues and a
radius has been resolved.
Surflex-Dock Customize Scoring Function

The customize scoring function utility was failing in SYBYL-X 2.0. The issue
has been resolved.
Timing for Protomol Generation

During protomol generation, each command is now executed in sequence to avoid
failures due to timing.
6 Docking Suite SYBYL-X 2.1

License Requirements for the Docking Suite
1.2 License Requirements for the Docking Suite

• Surflex-Dock Licensing
• License Requirements for the Docking Tutorials
1.2.1 Surflex-Dock Licensing

SYBYL-X Suite Licensing
SYBYL-X introduced a simplified licensing scheme:

• The “SYBYL” license, required to run SYBYL, allows the user to run
Surflex-Dock on a single CPU of any networked computer.
• The “SurflexDock_Local” license provides the ability for a single user to
take advantage of a single host computer with multiple CPUs.
• The “SurflexDock_Distributed” license provides the ability for a single
user to distribute jobs on any number of computers at a single site.
Module-Based Licensing
SYBYL continues to run with a license file issued before the SYBYL-X release.
Access to the Surflex-Dock functionality requires the following licenses:
Functionality License
To submit a Surflex-Dock job SurflexDock and SurflexDock_Interface

from SYBYL plus one SurflexDock_Engine for each
processor.
To submit a Surflex-Dock job SurflexDock plus one SurflexDock_
from the operating system com- Engine for each processor.
mand line
Additional features are accessible through the SYBYL interface to Surflex-

Dock, each requiring an additional license.
Generate 3D coordinates ConcordStandalone

Add hydrogens to the protein BioPolymer
Identify receptor cavities MOLCAD

License Requirements for the Docking Suite
Consensus scoring CScore—For fast CScore processing

from the SYBYL interface to docking,
you will need as many CScore licenses
as docking licenses.
1.2.2 License Requirements for the Docking Tutorials

When using SYBYL’s module-based license scheme the Surflex-Dock tutorial
makes use of a Biopolymer license in the protein preparation step.

2. Surflex-Dock Tutorial
This docking exercise uses thymidine kinase and 10 active ligands. Upon
successful completion of this tutorial, you will know how to use Surflex-Dock
to dock a series of ligands into the active site of a protein receptor. You can also
perform the validation test outlined at the end of the tutorial to verify that
Surflex-Dock enriches actives over inactives.
Licensing: See License Requirements for the Docking Suite on page 7.
Platform Note: Differences in mathematical rounding on different platforms

may yield slightly different results.
A Matter of Time: This tutorial includes a series of docking runs. The full set
requires about 30 minutes of personal time and 5 minutes of CPU time.

Perform a Simple Surflex-Dock Run
2.1 Perform a Simple Surflex-Dock Run

2.1.1 Get Started
1. It is always a good idea to clear the screen and reset the display before starting.
! > Delete Everything
! Click to reset all rotations and translations.
2. Make a local copy of the necessary files: the protein structure as retrieved from
RCSB and a file containing the structures of 10 active ligands.
! Type: cmd cp $TA_DEMO/surflex/1kim.pdb . (Include the space

and period at the end of the line.)
! Type: cmd cp $TA_DEMO/surflex/tk.hits . (Include the space
and period at the end of the line.)
2.1.2 Access Surflex-Dock and Prepare the Protein

3. Activate SYBYL’s interface to Surflex-Dock.
! Applications > Docking Suite > Dock Ligands
The Docking dialog is displayed (dialog description on page 32).
! Set the Docking Mode to Surflex-Dock Screen (SFXC) and press

Define.
The Surflex-Dock -Define SFXC File dialog is displayed (dialog description on

page 36).
This is the central dialog for the preparation of a Surflex-Dock run. Here you
will prepare the protein, define the active site, and generate the Surflex
protomol.
4. Read in the protein.
! In the Surflex-Dock -Define SFXC File dialog set the Protein

Structure’s pull-down to PDB then press the adjacent button to
retrieve 1kim.pdb.
1KIM, as stored in the RCSB repository, is a dimer. The file contains two
complete units related by symmetry. Each consists of a protein, ligand, sulfate
salt, and water molecules. This means that every atom has a symmetry-related
duplicate in the file.

Usage notes about using dimers (or any multi-unit protein) with Surflex-Dock:
• SYBYL assigns the first set of atoms to chain A and the second set to
chain B. However, because Surflex-Dock does not take chain names into
consideration, it perceives corresponding residues in the two symmet-
rical units as duplicate entries.
• You should only use those units in the protein that define or enclose the
active site.
• If the active site is completely defined within a monomeric unit, you
only need to use a single unit in Surflex-Dock. The other unit(s)
should be removed, as demonstrated in this tutorial. Using all the
units may lead to unexpected results since Surflex-Dock does not
consider chain names.
• If the active site is defined by multiple units, use those multiple
units. In this case, it is advised to generate the protomol using either
the Ligand mode (if a crystallographic ligand is present) or the
Automatic mode. Using the Residue mode may lead to unexpected
results since Surflex-Dock does not consider chain names.
5. Start the protein preparation.

! Press Prepare.
The Prepare Protein Structure dialog is displayed (dialog description in the

Biopolymer Manual).
6. Identify all the structures that you want to remove: all the residues in chain B,
the ligand in chain B, the co-crystallized salt in both chains, and all the waters.
You will keep only the residues and the ligand in chain A.
! Press Remove Substructures.
The Select Substructures dialog is posted.
! In the Substructures field, type B/* and press Apply.
Only the residues, co-crystallized salts and waters associated with chain B are
visible in the SYBYL window because a default option in the dialog is to Hide
Unselected.
! In the Other list, click on A/SO4_3 to add it to the selection.
! Press (Select All) to the right of the Water list.
All of the water molecules are selected.
! Press OK to delete all selected items.

7. Identify the ligand to be extracted from the cavity.
! Press Extract Ligand Substructures.
! In the Select Substructures dialog click on A/THM1.
Only the ligand atoms in chain A are visible in the SYBYL window because the
Hide Unselected option is on.
! Click OK to accept the selection.
The protein residues in chain A are displayed again. The ligand is colored
green-blue. It is still in the protein cavity and will be extracted later, when you
leave this dialog and return to the Surflex-Dock -Define SFXC File dialog.
8. Analyze the protein structure and prepare it for docking.
The Prepare Protein Structure dialog is displayed again, but items in the lower
half of the dialog are disabled. This is because you must first perform an
analysis.
! Press Analyze Selected Structure.
The analysis revealed problems with a few residues.
! Press the Show buttons associated with Repair Backbone, Repair

Sidechain, and Termini Treatment to locate the residues involved.
All residues identified by the analysis are located some distance from the cavity
and should not take any part in the docking operation.
Usage Note: Deciding whether to spend the time fixing those few residues
depends on how you intend to proceed with the docking. If you have a known
ligand and plan to use it to generate the protomol and if the problem residues
are far from the active site, you can simply proceed with the protein as is.
However, if the problem residues are close to the cavity, or if you intend to let
Surflex-Dock find the cavity and generate the protomol automatically, or if you
intend optimize the geometry of the entire protein prior to docking, it would be
best to spend some time to fully prepare the protein first.
9. Add all the hydrogens to the protein and ligand. These are necessary for
Surflex-Dock.
! On the Add Hydrogens press Add.
! In the Add Hydrogens dialog click OK to add all the hydrogens.

The hydrogens were added to the protein in the ideal geometry described in the
biopolymer dictionary’s residue files. A quick minimization step of these
hydrogens in the context of the protein will be performed later.
A few residues are reported as missing some their hydrogens. These are the
problem residues, all of them away from the cavity.
10. Prepare the molecule for a brief minimization using a suitable force field,
AMBER7 FF99. The corresponding atom types will be taken from the
dictionary for all residues, but 31 atoms are reported as not having their
AMBER/Kollman atom type assignment.
! On the Type Atoms line press Show.
All 31 ligand atoms are highlighted. They have the correct SYBYL atom types,
but this structure does not match any of the monomers defined in the dictionary.
! Press Fix next to Type Atoms.
! In the Assign AMBER Atom Types dialog set Atom Types to AMBER7
FF99 and press Assign Atom Types.
! Close the dialog.
The Prepare Protein Structure dialog still reports that 31 atoms do not have the
proper types. This is because other sets of AMBER and Kollman atom types
could be loaded on the ligand.
11. Orient the sidechain amides in all ASN and GLN residues to maximize
hydrogen bonding.
! On the Fix Sidechain Amides line press Fix.
12. Perform a focused minimization of the protein and its co-crystallized ligand.
! On the Staged Minimization line press Perform.
The amount of minimization to perform is a matter personal preference and

must be determined in the context of each docking project. In this tutorial only
the protein hydrogens and the ligand will be optimized, each for 10 iterations.
! The Stage Minimization dialog provides full customization. Set it as

follows:
- Toggle the Stages check boxes to keep only Minimize
Biopolymer Hydrogens and Minimize Ligands.
- Reset Steps to: 10 then press Apply.

- To select the AMBER force field, press Set Minimization

Details.
- In the Middle of the Minimize dialog press Modify.
- In the Force Field pull-down select AMBER7 FF99 and
press OK, then OK again.
! Back in the Staged Minimization dialog press OK to start the minimi-

zation.
Watch the minimization proceed in two brief stages. While the minimization is
proceeding the atoms are color coded according to the local strain energy (sum
of energy terms in which each atom is involved). When the molecule is once
again colored by atom types the minimization is complete.
13. This is all the protein preparation that is needed in the context of this tutorial
where the known ligand will be used to generate the protomol.
! Press Return to return to the Surflex-Dock preparation.
The ligand is extracted into a separate molecule area and also saved into a Mol2
file whose name is derived from the name of the protein (1kim) followed by the
string _ligand.
! Press OK in the Message dialog reporting that the ligand has been
named 1kim_ligand, extracted to M3, and saved to the 1kim_
ligand.mol2 file.
The prepared protein is saved in the 1kim_H.mol2 file.
2.1.3 Generate the Protomol

Consisting of molecular probes (CH4, C=O, N-H), the protomol is a represen-
tation an idealized ligand to which putative ligands will be aligned (see The
Surflex-Dock Protomol on page 77).
14. Specify the mode of construction for the protomol. The choices are:
• Automatic—Surflex-Dock finds the largest cavity in the receptor
protein.
• Ligand—A ligand in the same coordinate space as the receptor.
• Residues—User-specified residues in the receptor.
• Multi-Channel Surface—Use MOLCAD’s multi-channel functionality
to detect potential active site cavities. If multiple cavities are fond their
surfaces are displayed in blue and listed in a dialog where you can select
the surface that contains the active site.

In this tutorial you will use the extracted co-crystallized ligand.
! In the Surflex-Dock -Define SFXC File dialog, set the Protomol Gener-
ation Mode to Ligand.
15. Review the other settings.
Two parameters determine the extent of the protomol. Their default values are
adequate for most datasets.
• Threshold is a factor (from 0 to 1) determining how much the protomol
can be buried in the protein. The default is 0.50. Increasing this number
will decrease the volume. Using a very small number will greatly
increase the time it takes to generate the protomol.
• Bloat can be used to inflate the protomol and include nearby crevices.
The Prefix is a text string that reflects the conditions used to generate the
protomol. The prefix is used to name the file containing the protomol and the
Surflex-Dock control file. It is composed of:
• The name of the Mol2 file containing the prepared protein;
• A single letter representing the mode of generation: A(utomatic) or
L(igand) or R(esidues) or M(ulti-channel);
• The Threshold value;
• The Bloat value.
Usage Note: If the active site is an open channel, rather than an enclosed cavity,
remember to increase the Bloat value so that the generated protomol is large
enough to account for those open ends. If the Bloat value is too small, Surflex-
Dock may have difficulties defining the limits of the protomol at the ends of the
open channel. Increasing the Bloat value to 1 or 2 is often sufficient in most
cases.
16. Go ahead and generate the protomol based on the ligand’s coordinates.
! Press Generate.
It may take about a minute to generate the protomol, which is then stored in the
file 1kim_H-L-0.50-0-protomol.mol2.
17. Go ahead and generate the Surflex-Dock control file (.sfxc).
! Press OK to create the Surflex-Dock SFXC file.
The file takes its name from the protein and the conditions for the protomol
generation: 1kim_H-L-0.50-0.sfxc.

2.1.4 Specify the Ligands to be Docked and Submit the Job

The Docking dialog is active once more.
18. Indicate that the ligands are in a SLN file.
! Set the Ligands Source pull-down to SLN File.
! Enter tk.hits as the file name or use the file browser to locate the
file.
Usage Note: Surflex-Dock expects the ligands to be properly typed and proto-
nated as expected at physiological pH and their geometry to be optimized in any
arbitrary conformation. The most convenient way to achieve this is to press
Prepare to access the Ligand Preparation Setup dialog (see the Prepare
Ligands Manual for details). You may also use Concord to generate the
necessary 3D coordinates in the Surflex-Dock - Details dialog.
19. Check additional Surflex-Dock parameters in a separate dialog.
! In the Options section of the Docking dialog, press Surflex-Dock.
The Surflex-Dock - Details dialog appears (dialog description on page 47).
! Set the dialog as follows:

- 3D Coordinate Generation via Concord: If Necessary.
The input ligand coordinates are provided in 3D, so
Concord will not be needed.
- Allow Protein Movement: all options are off.
- General Parameters and Flags: automatically set for the
selected docking mode. See Surflex Docking Modes and
Default Options on page 53.
- Reference Molecule: with the format set to Mol2 access
the file browser and retrieve 1kim_ligand.mol2. It will be
used to calculate the similarity with each docked pose,
considering only non-hydrogen atoms.
! Press OK to return to the Docking dialog.
20. CScore — In the interest of speed CScore calculation will not be included in
this tutorial. In your own work, if you have access to CScore, you may want to
use additional scoring functions to evaluate the interactions between the ligand
and the receptor. For information see the CScore Details dialog on page 54.
! Toggle Perform CScore Calculations off if it is active.

21. Start the job.
! Surflex-Dock is fast, so you can set this small job to Run in Current
SYBYL Session.
! Enter tk as the job’s Name.
! Press OK to start the Surflex-Dock run.
The job’s name will be used to create a directory containing the complete output
for the docking run. All results will be found there.
Note: Actual performance depends on your hardware. For larger groups of

ligands, the job can be spread over a large number of processors (see License
Requirements for the Docking Suite on page 7).
2.1.5 Browse the Surflex-Dock Results

After completion of an interactive docking run, the results are posted automati-
cally in the Results Browser (dialog description on page 56). All other SYBYL
tools are available while this browser is open. To read in results from a remote
run use Applications > Docking Suite > Analyze Results then select the
jobname (tk) at the top of the dialog.
The docked ligands appear in the list in the center of the dialog. Surflex-Dock
produced multiple poses for each ligand. For each of the docked ligands, the
reported score is that of the pose with the highest score.
All ten ligands were docked successfully. They are listed in descending order of
total score values expressed as -log(Kd).
Examine the Highest Scored Ligand in the Active Site
22. Display the best scored ligand, TK_ganciclovir.

! Note that the Molecule radio button above the list is on.
This means that, when you select a line in the list, the corresponding ligand will
be displayed.
! Click on the first line in the list to highlight TK_ganciclovir.
The ligand is displayed as capped sticks. It is the best of 20 docked poses for
TK_ganciclovir.
Note that, by default, only the ligand’s polar hydrogens are displayed.
! To display all hydrogens:

- Click Visualization at the bottom of the Results Browser.

- In the Visualization Options dialog, toggle on Display Non-
Polar H.
- Leave the dialog open.
23. Display the protomol used by Surflex-Dock.
! In the View pull-down near the top of the Results Browser, select
1kim_H-L-0.50-0-protomol.mol21.
Hydrogen bonds, represented by dashed yellow lines, are displayed automati-

cally if a ligand is displayed as well as any of the items in the View pull-down.
This feature is particularly useful to visualize hydrogen bonds between a ligand
and the active site, but not while viewing the protomol.
! To undisplay the hydrogen bonds: in the Visualization Options dialog,
toggle off Display H-bonds.
! Rotate the combined structures to see how well the docked ligand
matches the probes that define the protomol.
24. Display the active site.
! In the Results Browser’s View pull-down, select tk_site.mol2
Note: This active site is not used during the run, but is created as a visual aid for
viewing results. The residues in this file are identified as those containing at
least one atom within 2.5 Å of any protomol atom.
! In the Visualization Options dialog:

- toggle on Display H-bonds;
- toggle off Display Non-Polar H;
- Close the dialog.
! Rotate the combined structures to see how well this docked ligand
fits into and interacts with the active site.
Compare the Docked Ganciclovir to the Experimental Ligand
25. Read in the experimental structure of the co-crystallized thymidine, which you
extracted earlier in this tutorial.
! Click on the SYBYL toolbar.
1. Long names may appear truncated in the menu.

! Select 1kim_ligand.mol2 in the Selection list.
! Select m4 as the molecule area to display it in then press OK.
The native ligand is displayed and colored blue-green.
26. Make the experimental ligand more visible by rendering it in capped sticks.
! Double-click any atom in the blue-green ligand then click .
! Clear the atom selection.
27. Hydrogen bond between active and docked ligands are displayed by the Results
Browser. This is not the case for the molecule you just read in. You must
display those manually:
! View > Hydrogen Bonds > Intermolecular
! Select M3:1kim and press OK.
! Select M4:1kim_ligand and press OK.
28. Compare the hydrogen bonding patterns made by both molecules.
! Use to toggle off and on the display of 1kim_ligand so that you

can see how both the reference ligand and the docked ganciclovir
engage in hydrogen bonding with some of the same residues.
Examine Other Docked Ligands and Their Poses
29. Clear all selection in the Results Browser.
! Unhighlight any selected ligand(s) in the list or click (clear).
30. Use the buttons to scroll through the docked ligands, one at a time.
! Click to view the highest scoring pose of the first ligand in the
list.
The ligand being examined is flagged with an asterisk in the list.
! Click again to view the highest scoring pose of the next ligand.
! Continue viewing each of the ligands.
! Scroll back to the top of the list so that the asterisk is on the TK_
ganciclovir line.

TK_ganciclovir is displayed, and there is an asterisk in front of its name in the

list.
! Use to toggle off the display of 1kim_ligand.
31. Look at multiple docked poses for each ligand. You can do so by combining the
the buttons and the Examine N Poses slider.
! Move the Examine N Poses slider to the right or use the right arrow
to show progressively more docked poses for TK_ganciclovir.
Although the slider can accommodate 30 poses, a maximum of 20 poses were

requested for this docking run, and the actual number of docked poses for each
ligand may be less than that.
! Set the slider to a small number of poses (such as 5).
The highest scoring poses of TK_ganciclovir are essentially identical. This is

not the case for all ligands.
! Click to scroll down the list and view the specified number of
poses for each ligand.
! When you are done, click to undisplay the docked poses for the
ligand being examined and remove the asterisk from the list.
Examine the Spreadsheet Associated with the Thymidine Docked Poses
32. Open all the results for TK_thymidine in a spreadsheet.
! In the Results Browser, activate the Table radio button above the list.
! Click on the TK_thymidine line in list to highlight it.
The docked poses for this and all other ligands were saved in a Multi-Mol2 file
named tk-results.mol2 in the job directory. The docked poses are also stored in
3D SLN format along with all the score values in the companion file,
tk-results.sln. Viewing the results for this ligand as a spreadsheet, named TK_
THYMIDINE, created the matching table file, TK_thymidine.tbl, also in the
job directory.
The spreadsheet contains one row for each of the 20 docked poses. The
numbers1 reported in the Results Browser for each ligand are those of the top-
scoring pose.
1. Differences in mathematical rounding result in slightly different results on different platforms.

The columns contain the following information:

• Total_Score = the total Surflex-Dock score expressed as -log(Kd). (See
The Surflex-Dock Scoring Function on page 79.)
• Crash = the degree of inappropriate penetration by the ligand into the
protein and of interpenetration between ligand atoms (self-clash) that are
separated by rotatable bonds. Crash scores close to 0 are favorable.
Negative numbers indicate penetration.
• Polar = contribution of the hydrogen bonding and salt bridge interac-
tions to the total score. The polar score may be useful for excluding
docking results that make no hydrogen bonds.
• Similarity = Surflex-Sim similarity between the docked pose and the
ligand provided as a reference for the Surflex-Dock run.
33. Close the TK_thymidine spreadsheet.
! To close the TK_thymidine spreadsheet, click on the highlighted line

in the Results Browser.
Save One Preferred Docked Pose
34. Save the top pose of the top-scoring ligand for use in a subsequent docking run
later in this tutorial.
! At the bottom of the Results Browser press Save Results.
Most of the default settings in the Save Results dialog will be used. With the
docked ligands sorted by descending total score values, the best pose of the
higher scoring ligand will be saved.
! Set the Save Results dialog as follows:
- First N (Descending Total_Score): automatically set to 1.
- Number of Poses per Ligand: automatically set to 1.
- Toggle on Strip Pose Number from Molecule Name.
- Output Formats: select only Multi-Mol2.
- Output Prefix: type ganciclo_top.
- Press OK.
The file ganciclo_top.mol2 contains the 3D coordinates of the top scoring

pose in the initial docking run. You will use it in the next docking run: Use
Placed Fragments to Guide Docking on page 23.

35. Close the Results Browser and clear the SYBYL screen.
! Close the Results Browser.
36. You may want to explore:

• Use Placed Fragments to Guide Docking on page 23
• Allow Protein Movement to Accommodate Docked Ligands on page 28
• Validation Study on page 30

Use Placed Fragments to Guide Docking
2.2 Use Placed Fragments to Guide Docking

2.2.1 Access Surflex-Dock and Retrieve the Docking File
! Set the Docking Mode to Surflex-Dock Screen (SFXC).
38. Retrieve the Surflex-Dock control file created for the first docking run. This file
includes the names of the Mol2 files containing the prepared protein, the ligand,
and the protomol. All these will be reused.
! Use the Filename [...] file browser to retrieve 1kim_H-L-0.50-0.sfxc.
2.2.2 Prepare the Placed Fragments

39. Indicate that you will be using placed fragments.
! Activate the Constraints check box and press Define.
The Surflex - Fragments Constraints dialog is displayed (dialog description on

page 42). It is automatically set to display the active site represented by the
residues containing at least one atom within 2.5 Å of any protomol atom.
40. Read in the highest scoring pose produced by the initial docking run. You saved
it in ganciclo_top.mol2 after exploring the results of that run.
! Press Import and retrieve ganciclo_top.mol2.
The ligand is displayed in capped sticks inside the active site. Hydrogen bonds
between the ligand and protein residues are shown as yellow dashed lines, and
those residues are labeled. These visual elements can be toggled on and off
within the dialog.
41. Fragment the ligand. With the Prefer Rings During Fragmentation option
below the list, fragments that include a partial ring structure will be automati-
cally expanded to the full ring during the fragment generation.
! Press to fragment the ligand.
A few fragments are listed in the dialog along with the number of atoms they
contain. Not all generated fragments are retained for inclusion in this list.
! Press to clear all selection in the list.

! Use the buttons to the right of the list to view each of the
fragments and decide which one(s) to use as hints for the next
docking run.
Usage Note: In your own work you may want to use the tools to the right of the
list to create additional fragments.
• —Access the Sketcher where you can modify the selected
fragment’s structure, add hydrogens, and modify its name.
• —Combine two or more selected fragments into a single new
fragment.
• —Filter the selected fragment(s) by the specified SLN string to
create new fragment(s).
• —Remove the selected fragment(s) from the list.
42. Select one fragment to be used as representative of the types of interactions you
want to favor between docked ligands and the active site.
! Clear all selection in the list then select TK_ganciclovir-frag-025,
which is H-bonded to TYR101 and GLN125.
43. Adjust the parameters that will direct the docking with placed fragments. The
most important of these are:
• the penalty associated with the deviation between docked poses and the
placed fragments.
• whether to dock only the ligands that include a substructural match to
the fragments
! Set the parameters in the dialog as follows:

- Penalty slider: 30.0. This is the most important parameter
when using placed fragments as a hint during docking. The
minimum value for the penalty to have any discernible
effect is 25.
- Require Fragments Match: off. Substructural match
between docked ligands and placed fragments is not
required.
- Include Hydrogens: off. Structural match to specific
hydrogens is irrelevant.
- Use Protomol: on. Docking will be performed using the
protomol as well as the placed fragments.

44. Indicate that only the selected fragment will be used and give a name to the
fragment constraint file.
! At the bottom of the dialog, click Include: Selected.
! In the field at the bottom enter 1kim-frags.mol2 as the name of the

fragment file.
! Press OK.
2.2.3 Submit the Docking Run with Placed Fragments

The Docking dialog is active once more.
45. Indicate that the ligands are in a SLN file.

! Enter tk.hits as the file name or use the file browser to locate the
file.
46. Check additional Surflex-Dock parameters in a separate dialog.
! This time set it as follows:

- Allow Protein Movement: all options are off.
- General Parameters and Flags: automatically set for the
selected docking mode. See Surflex Docking Modes and
Default Options on page 53.
- Reference Molecule: leave it blank.
47. Start the job.
! Set this small job to Run in Current SYBYL Session.
! Enter tk_ganciclo_frag as the job’s Name.
The job’s name will be used to create a directory containing the complete output
for the docking run. All results will be found there.

2.2.4 Browse the Results of the Constrained Docking Run

48. When the docking run with the placed fragment completes the results are posted
You can also load them at any time as follows:

Applications > Docking Suite > Analyze Results
Then load the tk_ganciclo_frag run.
! Notice that, as could be expected, the “ciclovir” ligands are ranked at

or near the top of the list.
Even though no substructural match to the placed fragment was required, these
three compounds can be oriented, more successfully than the others, to match
the constraining fragment.
! Scroll the list all the way to the right to bring that last two columns
into view.
FragIndex reports the ID number of the constraining fragment to which the

docked is most closely aligned. In this case, a single fragment was used, so a
value of 1 in this column indicates a match to that fragment. A value of -1
indicates that the docked pose does not align to any constraining fragment, but
was instead produced by alignment to the protomol.
FragRMSD reports the RMS distance between the constraining fragment and
the matching atoms in the docked pose. A value of -1 indicates no alignment.
! The ciclovir ligands stand out in the FragIndex and FragRMSD

columns.
! Scroll the list all the way back to the left.
49. Display the placed fragment that provided guidance during docking.
! In the upper-right corner of the dialog press Constraints.
! Select the fragment and press Close.
! Select the ciclovir ligands: TK_penciclovir, TK_ganciclovir, and TK_

aciclovir to display them.

2.2.5 Save the Top Three Docked Ligands

! With only the three ciclovir ligands highlighted in the list press Save
Results at the bottom of the dialog.
Most of the default settings in the Save Results dialog will be used. With the
selected ligands sorted by descending total score values, the best pose of each
ligand will be saved.
! Set the Save Results dialog as follows:

- Mode is automatically set to Selected.
- Strip Pose Number from Molecule Name: toggle it on
- Output Formats: select only SLN File
- Output Prefix: type ciclovir
- Press OK.
The file ciclovir.sln is created, containing the 3D coordinates of the top scoring
optimized pose for each of the ciclovir trio. You will use dock these in the next
docking run: Allow Protein Movement to Accommodate Docked Ligands on
page 28.
50. Close the Results Browser and clear the SYBYL screen.
! Close the Results Browser.
51. You may want to explore:

• Allow Protein Movement to Accommodate Docked Ligands on page 28

Allow Protein Movement to Accommodate Docked Ligands
2.3 Allow Protein Movement to Accommodate

Docked Ligands
2.3.1 Access Surflex-Dock and Retrieve the Docking File
! Set the Docking Mode to Surflex-Dock Screen (SFXC).
53. Retrieve the Surflex-Dock control file created for the first docking run. This file
includes the names of the Mol2 files containing the prepared protein and the
protomol. All these will be reused.
! Access the Filename [...] file browser and retrieve 1kim_H-L-0.50-
0.sfxc.
! Make sure that the Constraints option is off.
! Enter ciclovir.sln as the file name or use the file browser to

locate the file.
54. Set additional Surflex-Dock parameters in a separate dialog.

! This time set it as follows:
- Allow Protein Movement: toggle on Hydrogen and Heavy
Atoms.
- Fast Protein Flex: on to speed up the generation of protein
conformers.
- Covalent Force Field Weighting: the sliders are automati-
cally set to the most appropriate values. These allow signif-
icant movement of the protons to accommodate each
ligand’s binding preference, while preventing excessive
protein distortion.
- Number of Poses to Optimize: 2
- In the interest of speed reduce Maximum Number of
Poses per Ligand to 2.
- Reference Molecule: leave it blank.

Allow Protein Movement to Accommodate Docked Ligands
55. Start the double Surflex-Dock run.
! Set the job to Run in Current SYBYL Session.
! Enter tk_ciclovir_flex as the job’s Name.
The job’s name will be used to create a subdirectory containing the complete
output for the docking run. All results will be found there.
2.3.2 Browse the Results of the Flexible Docking Run

56. When the docking run with the additional protein flexibility step completes the
results are posted in the Results Browser.
You can also load them at any time as follows:

Then load the tk_ciclovir run.
The Results Browser provides access to two sets of scores because two consec-
utive Surflex-Dock runs are performed when protein flexibility is involved. You
can swap between the score sets via the Score pull-down menu:
• Base—The scores and poses resulting from a first, standard run.
• Protein Flexibility [PF-re]—The scores and poses resulting from the
second run, which allows protein movement and rescores the docked
poses. This list includes a Pose column because, for any given ligand,
the ranking of poses may be different before and after optimization.
57. Look at the optimized results.

! Make sure that the Score pull-down is set to Protein Flexibility [PF-
re].
! Select the top ligand in the list to display it as well as the surrounding
protein residues after movement.
58. To compare the relaxed active site display the original one.
! In the View pull-down near the top of the Results Browser, select tk_
ciclovir_flex_site.mol2.

Validation Study
2.4 Validation Study

Before performing prospective virtual screening of compound databases, the
method that will be used to perform the virtual screen needs to be validated.
Typically, a set of known actives and decoys are used as the dataset, and,
ideally, the virtual screening method will rank the results and place most of the
known actives among the top few percent of the overall dataset.
Two decoy datasets, taken from a publication by Pham & Jain (Ref. 1), are
available for use with the thymidine kinase ligands described in this tutorial.
• $TA_DEMO/surflex/Bissantz_Pham.hits
A set of decoys, described by Bissantz et al (Ref. 2), consist of 990
randomly chosen, non-reactive molecules taken from the Available
Chemicals Directory (ACD) and filtered according to drug likeness as
described by Pham & Jain. The file was filtered to remove duplicates,
reducing the dataset to 851 compounds. This file also includes the 10
thymidine kinase ligands used in the Surflex-Dock tutorial.
• $TA_DEMO/surflex/Zinc_Pham.hits
A set of decoys described by Pham & Jain, that consists of 1000
randomly selected compounds taken from the ZINC (Ref. 3) database
(drug-like subset). The file distributed with SYBYL also includes the 10
thymidine kinase ligands used in the Surflex-Dock tutorial.
Recommended Work Flow

1. Run Surflex-Dock on 1kim using the compounds in these datasets.
2. Save the top 5% docked ligands (by score) into a spreadsheet.
3. Sort the resulting spreadsheets based on row name (descending order for
Bissantz_Pham, ascending order for Zinc_Pham). You will see that most of
the thymidine kinase ligands appear at the top of the sorted spreadsheet.
If this was a prospective virtual screen, you could have assayed the top 5% of
your compounds (saving a large amount of time and resource) and retrieved
80% of the actives.
References
[1] Pham, T.A.; Jain, A.J. “Parameter Estimation for Scoring Protein-Ligand
Interactions Using Negative Training Data.” J. Med. Chem. 2006, 49,
5856-5868.
[2] Bissantz, C.; Folkers, G.; Rognan, D. “Protein-based virtual screening of
chemical databases. 1. Evaluation of different docking/scoring
combinations.” J. Med. Chem. 2000, 43, 4759-4767.
[3] ZINC, a free database for virtual screening, available for download from
http://zinc.docking.org/

3. Using the Docking Suite
• Prepare and Submit a Docking Job on page 32
• Define the Surflex-Dock Control File (SFXC) on page 36
• Select Substructures to be Removed from the Protein on page 39
• Define the Active Site on page 40
• Surflex-Dock with Fragment Constraints on page 42
• Surflex-Dock Details on page 47
• Perform CScore Calculations on page 54
• Analyze Docking Results on page 56
• Visualization Options
• Advanced Multi-Volume Expression
• Failed Ligand List
• Save Results

Prepare and Submit a Docking Job
3.1 Prepare and Submit a Docking Job

SYBYL provides a single interface for docking a collection of ligands in a rigid
protein or a protein ensemble. You may retrieve and prepare the protein and the
ligands from within the Docking dialog.
License availability allows you to select the docking engine and additional
features within the dialog: the use of pharmacophore constraints and the
docking of a combinatorial library. See License Requirements for the Docking
Suite on page 7.
Applications > Docking Suite > Dock Ligands
Descriptor File
Several docking engines are accessible through this dialog. If you have only
licensed a single docking engine (such as Surflex-Dock), ignore references to
the unlicensed applications.

Docking Mode Each of the Surflex-Dock modes maps to a set of

parameters. See Surflex Docking Modes and Default
Options on page 53.
• Surflex-Dock Screen (SFXC)—Use Surflex with
the screening parameter set to dock the ligands.
• Surflex-Dock Geom (SFXC)—Use Surflex with
the docking accuracy parameter set to dock the
ligands.
• Surflex-Dock GeomX (SFXC)—Use Surflex with
the more exhaustive accuracy parameter set to dock
the ligands.
Filename This field echoes the name of the file that is central to
the docking run. For Surflex-Dock, a . sfxc file.
Press the [...] button to access a file browser and
retrieve an existing file or press the Define button to
start the definition process.
Define Access the Surflex-Dock - Define SFXC File dialog to
create or modify a . sfxc file for a single receptor in a
molecule area or read in from a file in Mol2 or PDB
format.
Using Surflex-Dock Placed Fragments to Constrain a Docking Run
Constraints Activate the check box to use placed fragments during

the Surflex-Dock docking run.
Filename Press the […] button to access a file browser and
retrieve an existing .mol2 file containing one or more
placed fragments. Alternatively, press Define to gener-
ate those fragments.
Define Access the Surflex - Fragment Constraints dialog where
you can define placed fragments, select those to be used
during the docking run, and adjust several associated
parameters.

Ligands
Ligand Source Designate the source of prepared ligands (ionized as

appropriate):
• SLN File—a file in SLN format such as that
produced by a UNITY search (.hits or .sln).
• cSLN File—a file in compact SLN format that
describes multiple variations at more than one site.
This option is available only for Combinatorial
docking.
• Spreadsheet File—a SYBYL spreadsheet saved
to file (.tbl).
• Mol2 File—a SYBYL Mol2 file.
• SD File—a file in SD format (.sdf).
• SMILES File—a file containing SMILES strings
(no default extension)
• SYBYL Database—a directory of Mol2 files. The
directory has a .mdb extension.
• Molecule Area(s)—molecule area expression.
This option is accessible only if there is at least one
molecule on the screen.
• Open Spreadsheet—an already open spread-
sheet.
Enter the file name or molecule area expression in the
associated field or press the adjacent button to access
the appropriate browser.
Open Data as View the ligands in a spreadsheet. This option is avail-
Spreadsheet able for all formats except cSLN File.
Once the spreadsheet is open, you may select rows and
use only those in the docking run. If no rows are
selected, all will be used.
Note: Once a spreadsheet has been opened, it cannot be
closed until the Docking dialog is closed. You may,
however, select another ligand source for the docking
run.
Prepare After reading in the ligands from a file, access the
Ligand Structure Preparation tool where you can make
sure that all the ligands are adequately prepared for
docking (see the Prepare Ligands Manual for details).
Surflex-Dock requires that all input molecules be proto-
nated at physiological pH including non-polar hydro-
gens.
Note: Different isomers of the same compounds must
have different names.

Options
Surflex-Dock Access the Surflex-Dock - Details dialog.

Runtime Insert options into the command that will be executed
when you submit the job. Access the Surflex-Dock
Advanced Configuration - Runtime Parameters dialog.
Perform CScore Whether to compute additional scores and generate
Calculation consensus scores. This option is on by default is you
have access to CScore (see License Requirements for
the Docking Suite on page 7).
CScore Details Access the CScore Details dialog and select the addi-
tional scoring functions and specify whether structure
relaxation should occur. See the CScore Theory in the
CScore Manual for a description of the other scoring
functions.
Job Submission
Mode of operation Specify how and where to run the job:

• Run in Current SYBYL Session — Run the job
interactively. SYBYL will become active again as
soon as the job completes.
• Multiple Machines — Display a table of the
machines listed in your network_map file, along
with the number of Cores and Threads for each
machine. Check the boxes for the machines to run
the job across. Click in the Threads cell and enter
the number of threads (processors) to use on a
particular machine.
• <current host> — Run the job as a background

process on the machine running SYBYL.
• <host names> — Run the job on another machine
defined in your network_map file.

Nice Level Number passed to the system’s nice command to

adjust the job’s priority level. The higher the number,
the lower the priority.
# Procs The total number of selected threads (processors).
Name Enter the name to use for the subdirectory that will be
created containing the complete output for the docking
run.
Additional Information:
Analyze Docking Results on page 56
3.1.1 Define the Surflex-Dock Control File (SFXC)

The Surflex-Dock control file (.sfxc) contains information about the protein and
the method used to generate the protomol.

In the Docking dialog:
• set the Docking Mode to one of the Surflex-Dock modes;
• press Define on the next line.
In addition to protomol generation, this dialog provides access to the tools

necessary to prepare the protein and ligands before docking. All input molecules
must be protonated as expected at physiological pH including non-polar
hydrogens.

Protein Structure
Input Format How to read in the protein structure: Mol2 file, PDB
file or Mol Area.
Protein Source Enter the name of the input file or molecule area con-
taining the protein receptor or use the adjacent browser
to retrieve it.
Prepare Access the Prepare Protein Structure dialog to prepare
the protein structure for docking with Surflex. In partic-
ular, the protein must be protonated at physiological pH
including non-polar hydrogens, and the active site must
not contain any docked ligand.
Protomol Generation
Mode How to begin the construction of the protomol:

• Automatic—In a protein with multiple cavities or
binding sites, the automatic protomol generation
selects the largest cavity.
• Ligand—If the protein structure included a ligand,
the ligand’s position can be used. Make sure that all
ligand atoms are connected properly.
This option is recommended when working with a
multimer (dimer/trimer/etc.) where the active site is
defined by multiple units and a crystallographic
ligand is available.
• Residues—With the source set to Mol Area, press
the [...] button to access the Define Active Site
dialog and identify the residues you want to use to
generate the protomol. You may also read the
residue names from a Text File.
• Multi-Channel Surface—Use MOLCAD’s multi-
channel functionality to detect potential active site
cavities. If multiple cavities are found their surfaces
are displayed in blue and listed in a dialog where
you can select the surface that contains the active
site. The protomol is generated from the residues
that are within 4.5 Å of the surface.
Note: The protomol is not meant to be an absolute
docking envelope. Its purpose is to direct the initial
placement of the ligand during the docking process.
Docked ligands are scored in the context of the recep-
tor, not in the context of the protomol.

Source • Mol Area—If the ligand is in a molecule area, use

the [...] button to designate it. You may also use this
option to identify the residues that define the cavity.
• Mol2 File—If the ligand is in a Mol2 file use the
[...] button to retrieve a file with a .mol2 extension.
• Text File—You can store the residue names, one
per line, in a .txt file.
Threshold One of the two parameters determining the extent of the
protomol. This factor (between 0.01 and 0.99) indi-
cates how much the protomol can be buried in the pro-
tein. The default of 0.50 is adequate in most
circumstances. Increasing this number will decrease the
volume. Using a very small threshold value greatly
increases the time it takes to generate the protomol.
This feature corresponds to the option:
-proto_thresh number.
Bloat This second parameter provides a way to inflate the
protomol. Use the slider to specify the number of Å (0–
10) used to expand the protomol in 3D.
Changing this parameter may affect the protomol’s vol-
ume in the following situations:
• With a longer distance, the protomol can reach into
crevices.
• If the active site is a channel, rather than a cavity,
longer distances may be required to better define
the protomol at the open ends of the channel.
According to the program’s author, a smaller protomol
is generally better than a larger one.
This feature corresponds to the option:
-proto_bloat distance.
Prefix This string is assembled automatically and reflects the
conditions used to generate the protomol. The string
consists of the following elements separated by
hyphens:
• The base name of the Mol2 file containing the
protein as specified at the top of the dialog.
• A single letter representing the mode of generation:
A(utomatic) or L(igand) or R(esidues) or M(ulti-
channel).
• The Threshold value.
• The Bloat value.
For example: pdb4dfr_H-A-0.50-0

Generate Press this button to generate the protomol based on the

conditions specified in the dialog. Upon completion, a
Connolly surface will be displayed around the protomol
Surflex-Dock Input Files
Protomol The name of the Mol2 file containing the protomol con-
sists of the Prefix followed by “-protomol” and a
.mol2 extension.
Edit Press this button to access the SYBYL Sketcher
(described in the SYBYL Basics Manual). You can
then add, delete, or modify the atoms that make up the
protomol.
SFXC File The name of the Surflex control file consists of the
Prefix and a .sfxc extension.
3.1.2 Select Substructures to be Removed from the Protein

When preparing the receptor protein for a Surflex-Dock run it is necessary to
extract the ligand (if any) from the active site cavity as well as other structures
that would be displaced by the ligands to be docked.
In the Surflex-Dock -Define SFXC File dialog press Prepare.

Then in the Prepare Protein Structure dialog (Biopolymer Manual):
• Press Extract Ligand Substructures
• Or press Remove Substructures

Select from Sub- All the substructures in the protein are sorted by type
structure Lists for easier selection. Names are all preceded by the
name of the chain to which they belong.
Banks of buttons (select all, invert selec-
tion, clear selection) assist in each selection. Clicking a
second time on any item unselects it.
• Residues—List of all the amino acid residues.
• Other—List of the substructures that are not amino
acid residues or water. Typically found here are
ligands and cofactors.
• Water—List of co-crystallized water molecules.
Selection Enter the radius (in Å) surrounding already selected
Radius structure(s). All residues for which at least one atom is
within the selection radius are included and highlighted
in the list. The default radius is 0.1 Å, so that only the
designated substructures are selected.
Hide Unselected By default, only the selected substructures are shown.
These can be protein residues, cofactors, ligands, and
co-crystallized waters.
Label Selected Whether to label the selected substructures.
Pick from Pick one of more substructures directly from the screen
Screen of specify them via the Substructure Expression dialog,
a variant of the Atom Expression dialog where the
smallest unit is a substructure.
Clear All Clear the selection no matter how it was made.
Substructures This field echoes the selection made in the dialog. You
may also edit this field directly.
3.1.3 Define the Active Site

Identify the receptor’s active site.
In the Surflex-Dock - Define SFXC File dialog set the Protomol Generation
Mode to Residues and press the [...] button nearby.
Note: Surflex-Dock uses the residues identifying the active site for the sole
purpose of generating the protomol. The jobname_site.mol2 file displayed in
the Results Browser is created as a visual aid, and its residues are identified
based on the protomol coordinates.

Selection Methods
Ligand Based Select the Mol2 file containing the ligand of interest.
Pick from Pick one of more substructures directly from the screen
Screen of specify them via the Substructure Expression dialog,
a variant of the Atom Expression dialog where the
smallest unit is a substructure.
Select from Sub- All the substructures in the protein are sorted by type
structure Lists for easier selection. Names are all preceded by the
name of the chain to which they belong.
Banks of buttons (select all, invert selection,
clear selection) assist in each selection. Clicking a sec-
ond time on any item unselects it.
• Residues—List of all the amino acid residues.
• Other—List of the substructures that are not amino
acid residues or water. Typically found here are
ligands and cofactors.
• Water—List of co-crystallized water molecules.

Selection Tools
Selection Enter the radius (in Å) surrounding the structure(s) at

Radius the center of the active site. All residues for which at
least one atom is within the selection radius are
included.
For Surflex-Dock, the default is 3 Å around the selected
substructures. Surflex-Dock will then use those resi-
dues to generate the protomol.
Note: The jobname_site.mol2 file displayed in the
Results Browser is created as a visual aid, and its resi-
dues are identified based on the protomol coordinates.
As such it may be different from the site defined in the
current dialog.
Hide Unselected By default, only the selected substructures are shown.
These can be protein residues, cofactors, ligands, and
co-crystallized waters.
Label Selected Whether to label the selected substructures.
Clear All Clear the selection no matter how it was made.
Substructures This field echoes the selection made in the dialog, but
without the expansion specified by the Selection
Radius slider. You may also edit this field directly.
To use only the substructures listed in this field, set the
slider to 0.1 Å.
3.1.4 Surflex-Dock with Fragment Constraints

Generate and select the placed fragments to be used to constrain the docking
run. Specify the associated parameters [Ref. 1].

• set the Docking Mode to one of the Surflex-Dock modes;
• define or retrieve a Surflex-Dock .sfxc file;
• activate Constraints and press the adjacent Define button.
Usage Note: Use this dialog to create a master list of fragments and save them
all in a multi-Mol2 file. In subsequent docking runs, import the master file into
the dialog, select the fragments of immediate interest and include only those in
the fragment constraint file that will be used for more focused docking.

Source
Press Import to retrieve small molecules and fragments in a variety of file
formats. Each imported molecular entity is added to the list below, where you
can display and modify it as needed.
Usage Notes:
• Each fragment that will be used to constrain the docking run must have
its atoms and bonds typed properly. It must share Cartesian coordinate
space with the protein and be oriented to form the desired interactions
with residues in the active site.
• To import a collection of ligands from multiple protein-ligand
complexes you must align the proteins before accessing the Docking
dialog. Backbone, sidechain, and water atoms will be automatically
excluded. All remaining substructures will be imported, coordinates

unchanged, as individual fragments.

To prepare and align the protein- ligand complexes:
• Read in all the protein-ligand complexes of interest.
• Make sure that all the proteins have a comparable number of residues
and that these are all in a single chain. Keep all the ligands and
delete extraneous protein features, if any.
• Align all proteins onto one of them:
Biopolymer > Compare Structures > Align Structures By
Homology
• Save the aligned protein-ligand complexes to a single file in Mol2
format.
Visualize
To help in the visualization and selection of placed fragments you may choose
to display:
Protein Display a transparent surface around the entire protein.

Active Site The residues are identified as those containing at least
one atom within 2.5 Å of any protomol atom.
Protomol Display the protomol envelope as a transparent sur-
face. See Define the Surflex-Dock Control File (SFXC)
on page 36 for modes of protomol generation.
Hydrogen Hydrogen bonds that can be formed between displayed
Bonds fragments and atoms of the Active Site are represented
as dashed lines and the interacting residues are labeled.
Use this visual element to select the placed fragments
that will constrain the docking run.
Fragments
Fragment List List of fragments that can be used to constrain the

docking run. You may use the column headers to sort
the list by fragment name or atom count.
Fragment the selected structure(s), taking into account
the specified preference for ring-containing fragments.
Not all generated fragments are retained for inclusion in
the list.

Access the Sketcher where you can modify the selected

fragment’s structure, add hydrogens, and modify its
name. Upon exiting the Sketcher the structure is auto-
matically submitted to a cleanup that by default fixes
bond lengths and angles to match those in the SYBYL
parameter files and scans acyclic bonds to escape
atomic overlaps.
Combine selected fragments into a single new frag-
ment.
Filter the selected fragment(s) by the specified SLN
string to create new fragment(s).
Remove the selected fragment(s) from the list.
Buttons to assist in selecting fragments in the list:

select all, invert selection, clear selection.
Move to the next or previous fragment in the list and
display it.
Prefer Rings Whether to favor the creation of ring-containing frag-
During ments.
Fragmentation • On (+misc_ring)—Fragments that include a
partial ring structure are automatically expanded to
the full ring during the fragment generation. This is
the default in the dialog.
• Off (-misc_ring)—This is the default when using
the standalone surflex-dock.exe.
Match Parameters
Require Frag- Whether to dock only the ligands that include a sub-
ment Match structural match to the fragment.
• Off (-fskip)—All ligands are docked. Those that
have no matching fragment are docked in the
normal fashion. This is the default.
• On (+fksip)—Screen the input ligands based on a
specific structural moiety and submit to docking
only those that match.
Include Hydro- Whether to force all hydrogens that exist in the frag-
gens ment to be matched explicitly by the ligand to be
docked.
• Off (-fhmatch)—All fragment hydrogens are
ignored. This is the default.
• On (+fhmatch)—Provide fine user control over the
structural moiety to match by including specific
hydrogens.

Coarse Confor- Whether to perform a coarse or fine (default) conforma-

mational Search tional search when using fragment constraints.
This feature (off by default) corresponds to the +/
-fcoarse option.
Use Protomol Whether to dock using the protomol in addition to the
placed fragments.
This feature (on by default) corresponds to the
+/-fdockreg option.
Penalty for Devi- Provides a method to force the matched ligand sub-
ating From Frag- structure to the position of the placed fragment. The
ment penalty is expressed in units of pKd/Å2.
A label above the slider helps guide your selection:
• None: 0 <= penalty <= 5
• Light: 5 < penalty <= 25
• Moderate: 25 < penalty <= 75. The recommended
minimum to have any observable effect is 25.
• Heavy 75 < penalty <= 100
This feature corresponds to the -cpen n option.
Rotatable Bond Depth
Initial After each ligand to be docked is aligned on the frag-

ment position its conformational space is enumerated
from the fragment outward by the specified number of
rotatable bonds.
This feature corresponds to the -fidepth n option
with a default of 3 rotatable bonds and an allowed
range from 1 to 10.
Recursive For each particular depth, if the conformational change
to the parent pose affects the geometry of the atoms
within the matched substructure, the alignment is
recomputed, and the new conformation is scored with
respect to the similarity to the protomol. The best scor-
ing poses are subjected to local optimization.
For flexible molecules this process iterates from from
the highest scoring poses after each local optimization.
This feature corresponds to the -frdepth n option
with a default of 3 rotatable bonds and an allowed
range from 1 to 10.
Fragment Constraint File
All/Selected/ Store in a Mol2 file the fragment(s) to be used to con-

Unselected strain the docking run. Use All the fragments in the list
or only some based on the current selection.

3.1.5 Surflex-Dock Details

Specify the maximum number of docked structures and modify several of the
parameters used by Surflex-Dock [Ref. 1]. The default parameters depend on
the selected docking mode (see Surflex Docking Modes and Default Options on
page 53).

• set the Docking Mode to any of the Surflex-Dock modes;
• press Surflex-Dock.
Additional parameters may be specified via the Surflex-Dock Advanced Configu-

ration - Runtime Parameters dialog.

Input Options
3D Coordinate This option is essential if the ligand file contains only

Generation 2D coordinates. (See License Requirements for the
(Concord) Docking Suite on page 7.)
• If Necessary—This option is on by default, which
guarantees that if the input ligands have 2D coordi-
nates, they are converted to 3D.
• Generate Coordinates—Forces the generation of
3D coordinates.
• Bypass—Uses the input ligands as provided.
Results Optimization
Allow Protein Whether to allow flexibility of protein atoms whose van

Movement der Waals surface distances from ligand atoms are
< 4 Å and adapt the active site conformation to the
docked ligand. Protein atoms that chelate metal ions
and the metal themselves are never allowed to move.
• Hydrogens—Whether to optimize hydroxyls and
thiols as well as all protons in the protein pocket.
This feature corresponds to +/-pflex and is off by
default.
• Heavy Atoms—This feature corresponds to +/
-hprot and is off by default. Hydrogen flexibility
must be activated first.
Protein movement takes place in a second Surflex-Dock
run, which produces an additional score set, named Pro-
tein Flexibility [PF-re] and accessible in the Results
Browser.
Specify Flexible Used only during a docking run that includes protein
Residues movement to identify a text file listing the residues (one
per line) that are allowed to be flexible.
This feature corresponds to the -pflexparam option
and is used with +pflex.
Fast Protein Used only during a docking run that includes protein
Flex movement to optionally perform faster rescoring using
less thorough protein flexibility.
This feature corresponds to the +/-rescorefast
option and is used with rescore_multi.

Covalent Force Relative strengths of the covalent force field when

Field Weighting applied to:
Ligand—Weight of the ligand covalent force field.
This feature corresponds to the -lcov n option with a
default of 1.0 and a useful range from 0.01 to 1.0.
Protein—Weight of the protein covalent force field.
This feature corresponds to the -pcov n option.
Within a useful range from 0.01 to 1.0 the recom-
mended values are:
• 0.1 if only protein hydrogens are flexible. This
allows significant movement of the protons to
accommodate each ligand’s binding preference.
• 0.6 if the protein heavy atoms are also allowed to
move. This prevents excessive protein distortion.
Number of The maximum number of poses to optimize and rescore
Poses to Opti- for each ligand after a docking run that includes protein
mize movement.
The feature corresponds to the -maxposes n option
and defaults to 10.
General Parameters
Additional Start- When this value is 0 (used in standard and screening

ing Conforma- modes), ligands are docked based on the supplied con-
tions per formation, which almost always affects the docking
Molecule score.
Surflex-Dock can dock ligands from a specified number
of starting conformations that are generated by random
perturbation of the position and conformation of the
supplied ligand followed by bump relaxation. The best
results are reported by combining the independent
docking runs. For flexible molecules, multiple starting
conformations will often yield higher-scoring and more
consistent results. The values used when docking for
accuracy are 4 (Geom) and 6 (GeomX).
The best return on time investment for this parameter is
5, and the recommended maximum is 10.
This feature corresponds to the -multistart n
option.
Angstroms to By default, the search grid extends 6 Å beyond the pro-
Expand Search tein dimensions. Increasing this values is useful when
Grid docking surface-bound ligands.
This feature corresponds to the -grid_bloat n
option.

Max Conforma- The maximum number of conformations per fragment

tions per Frag- to be submitted to the docking procedure. The default
ment value is 20.
This feature corresponds to the -maxconfs n option.
Max Number of The maximum number of rotatable bonds in any input
Rotatable Bonds ligand. The default value is 100. Terminal symmetrical
per Molecule groups like CH3 and NH3 are not rotated.
This feature corresponds to the -maxrot n option.
Flags
Include Self- Whether to include the non-covalent intramolecular

Scoring Term component of the scoring function.
This feature (off by default) corresponds to the
+/-self_score option.
Consider Ring Whether to allow ring flexibility when generating the
Flexibility molecular fragments. Conformations taken from a
small, generic library are applied to each 5, 6, or
7-membered ring, regardless of atom types. The result-
ing conformations are minimized using a BFGS quasi-
Newton method and an internal Dreiding force field.
This option is active by default when docking for more
exhaustive accuracy (GeomX).
This feature corresponds to the +/-ring option.
Rigid Molecule Whether to restrict the flexibility of the ligands and
Search dock them in their initial conformation. By default
(off), the Surflex-Dock procedure explores each
ligand’s conformational space.
This feature corresponds to the +/-rigid option.
Soft Grid Treat- Whether to allow the ligand to leave the bounds of the
ment search grid, which is identified by the location of the
nearby protein atoms.
• By default (a hard grid), ligand atoms that venture
outside those bounds incur a large penalty. Under
this treatment, large ligands that cannot fit will have
large negative scores.
• Under the soft grid treatment, the space beyond the
edge is considered to be empty, which allows ligand
atoms to venture out of bounds without penalty.
For most ligands and most grids, the treatment of soft
or hard will not affect docking.
This feature corresponds to the +soft_box/-soft_
box option.

Pre-Dock Mini- Whether to optimize the geometry of the ligand(s)

mization before docking. Optimization uses a BFGS quasi-New-
ton method and an internal Dreiding force field.
This force field does not make use of atom types.
Instead, it uses the atomic elements and approximates
the hybridization by examining the number of con-
nected atoms and lone pairs that occur at any given
atom.
This feature corresponds to the +/-premin option.
Post-Dock Mini- Whether to optimize the geometry of the ligand(s) after
mization docking (see Pre-Dock for additional information).
The ligand is minimized in the context of the receptor,
not in the context of the protomol.
This feature corresponds to the +/-remin option.
Molecule Frag- Whether to disable the fragmentation of the input
mentation ligand. Fragmentation (which is used by default)
reduces the docking time while providing a good repre-
sentation of the conformational space.
This feature corresponds to the +/-frag option.
Spin Alignment
Activate Spin How to select the corresponding sets of observation

Alignment points between the molecule to the aligned and the tar-
Method get.
• On (+, default)—Use the newer and more robust
spin alignment method which uses a subsampled set
of observation points to produce an alignment that
places no constraint on the rotation around the axis
of the normal vector from the observers to the
molecule.
• Off (-)—Use the original alignment method which
looks for triplets of matching observation points
that match in terms of what each observer is seeing
and in terms of the edge lengths.
This feature corresponds to the +/-spinalign option.
Density of Used with the spin alignment method. The higher the
Search number the denser the search. The default value
depends on the selected docking parameter set: screen-
ing (3.0), accuracy (6.0) or exhaustive accuracy (9.0).
This feature corresponds to the -spindens n option.

Number of Spins Used with the spin alignment method to control the
per Alignment rotation around the normal vector from the observer to
the molecule. Default = 12.
This feature corresponds to the -nspin n option.
Output Options
All poses for all successfully docked ligand are stored in a single Multi-Mol2
file.
Maximum Num- Enter the maximum number of docked poses to be

ber of Poses per saved by Surflex-Dock for each ligand. The default is
Ligand 20, but the screening mode reduces it to 3. The limit is
100 poses.
This feature corresponds to the -ndock_final n
option.
Minimum RMSD The RMS distance between final docked poses for each
Between Final docked ligand must be greater than the specified value.
Poses In the default and screening modes the default is
0.05 Å. When docking for accuracy (Geom and
GeomX) the default value is 0.5 Å.
This feature corresponds to the -div_rms n option.
Reference This option is useful to compare the docked poses to
Molecule the crystal structure of a single ligand.
In the pull-down, select whether the reference structure
will come from a Mol2 File or a Molecule Area, then
enter the file or molecule area name in the field. Press
the adjacent button to access the appropriate browser.
If a reference molecule is specified, it must share coor-
dinate space with the protein. It is used by Surflex-
Dock to calculate the similarity with each docked pose,
considering only non-hydrogen atoms. These numbers
are reported in the Similarity columns in the ligand’s
table file of docked poses and in the Results Browser
for each ligand’s top-scoring pose.

Surflex Docking Modes and Default Options
Table 1 Parameter sets for the various docking modes in the SYBYL
interface (left column) and at the Surflex-Dock command line.
Parameters Docking Modes

(Surflex-Dock -
Details Dialog) Default Screen Geom GeomX
-pscreen -pgeom -pgeomx

Pre-dock minimi- +premin +premin +premin +premin
zation
Post-dock minimi- +remin +remin +remin +remin
zation
Max # -ndock_final 20 -ndock_final 3 -ndock_final 20 -ndock_final 20
poses/ligand
Min RMSD -div_rms 0.05 -div_rms 0.05 -div_rms 0.5 -div_rms 0.5
between poses
Additional starting -multistart 0 -mulstistart 0 -multistart 4 -multistart 6
conformations
Alignment method +spinalign +spinalign +spinalign +spinalign
-nspin 12 -nspin 12 -nspin 12 -nspin 12
-spindense 3 -spindense 3 -spindense 6 -spindense 9
Surflex-Dock Runtime Parameters
This dialog is brought up by pressing the Runtime button in the Docking dialog
(in Surflex-Dock mode). It allows you to insert options into the command that
will be executed when you submit the job.
For a list of options and their usage:

! Open a system shell with the SYBYL-X Environment defined as
described in the SYBYL Basics Manual.
! Type: surflex-dock.exe
See BioPharmics’ Surflex Manual for descriptions of the command line options.
The following option may be of interest:

-cpen number
Overrides the penalty value set in the Surflex - Fragment Constraints dialog.

Warning: No validation will be performed when you close the Runtime Param-
eters dialog. The options you enter will be used “as is.” In addition, runtime
parameters supersede the options specified in the Surflex-Dock - Details dialog.
3.1.6 Perform CScore Calculations

CScore (Consensus Score) integrates a number of popular scoring functions for
ranking the affinity of ligands bound to the active site of a receptor. The
strengths of individual scoring functions combine to produce a consensus that is
more robust and accurate than any single function for evaluating ligand-receptor
interactions.
Licensing: See License Requirements for the Docking Suite on page 7.
Access: In the Docking dialog, press CScore Details.
Parameters The default parameter file to use with the CScore pro-
gram itself ($TA_MOLTABLES/flexx_cscore.par).
Read about this parameter file in the CScore Manual.
Relax Structure Relax the protein/ligand pair, using the various options
in the associated parameter file.
Score Relaxed Generate additional CScore scores for the relaxed pro-
tein/ligand pair. This option is available only if the
Relax Structure box has been checked.
Scoring Func- Toggle on or off the various scoring functions
tions (described in the CScore Manual) to compute additional
scores and create the corresponding columns in the
spreadsheet. The consensus score is then generated
from the combination of these scores and the score
computed by the selected docking engine.

CScore Direc- CScore files (.cso) are written to a subdirectory (by

tory default CScore) of the job directory unless a file
named CScoreOutputLocation (also in the job
directory) specifies a different location. If that file does
not exist, the .cso files are expected to be in the job
directory.

Analyze Docking Results
3.2 Analyze Docking Results

3.2.1 The Results Browser
Use the Results Browser dialog to analyze results of jobs submitted via the
Docking dialog.
Notes:
• All other SYBYL tools are available via the menubar or command line
while this browser is in operation.
• The rendering and color of molecules displayed via the Results Browser
may be customized. See Customizing the Rendering and Colors of
Displayed Results on page 62.

Jobname Press the […] button to access a directory browser and

select the run to be analyzed. The jobname (including
path) is displayed in the field. Multiple jobs can be ana-
lyzed sequentially in a single session.
Usage Note: If the Results Browser fails to determine
the type of job whose results must be displayed, it will
prompt you (in a dialog) to select among all Docking
methods licensed at your site.
View Items not in the List
Protein Display in the first available molecule area the selected

protein. Long names may be truncated in the list.
• For a docking run on a single protein, only that
protein is listed.
• For a run on an ensemble receptor with combina-
torial docking, only the first protein can be
displayed.
Site Display in the first available molecule area the selected
active site. Long names may be truncated in the list.
• For a docking run on a single protein, only one site
is listed.
• For Surflex-Dock, the site file is not used during the
run, but is created as a visual aid for viewing
results. The residues in this file are identified as
those containing at least one atom within 2.5 Å of
any protomol atom. As such this site may be
different from a user-specified list of residues used
to guide the protomol generation in preparation for
the Surflex-Dock run.
Reference Display in the first available molecule area the mole-
cule provided (optionally) as a reference at the bottom
of the Surflex-Dock Details dialog.
Protomol Display in the first available molecule area the proto-
mol used in a Surflex-Dock run. Long names may be
truncated.
The protomol is not meant to be an absolute docking
envelope. Its purpose is to direct the initial placement
of the ligand during the docking process. Docked
ligands are scored in the context of the receptor, not in
the context of the protomol.
None Do not display anything from within this list.

View Additional Information
Constraints For a Surflex-Dock run with placed fragments, access

the Surflex-Dock: Fragment Constraints dialog to dis-
play and color the fragments.
List Size
Ligand Index This slider determines the position in the total list of the
ligand at the top of the current view. This feature is par-
ticularly useful for large ligand sets when used in com-
bination with the Max Listed slider.
Max Listed This slider determines the number of compounds in the
visible list. The first compound is determined by the
Ligand Index slider.
Scroll through the list, one page at a time. The size of
the visible portion of the list is defined by the Max
Listed slider.
Sliders
Ligand Index The position in the total list of the ligand at the top of
the current view. Use the slider or its < and > buttons to
change this number. This feature is particularly useful
for large ligand sets when used in combination with the
Max Listed slider.
Max Listed The number of compounds in the visible list. The first
compound is determined by the Ligand Index.
Examine N This slider is active only when a docked or aligned
Poses ligand is being examined via the buttons and
only for the Base score set. Move the slider to the right
to display an increasing number of poses for that
ligand. The maximum number of poses per ligand is
specified at run time. Fewer poses may be found for
any of the ligands.
Score Sets
For details of score values refer to Surflex-Dock Values in the Results Browser
on page 63.
Base The set of scores resulting from the Surflex-Dock run.

Protein Flexibil- The second set of scores resulting from a docking run
ity [PF-re] that includes protein flexibility. The option to Allow
Protein Movement must be specified in the Surflex-
Dock Details dialog before the run.
Selection Action
Molecule When this radio button is active any selection in the list
toggles the display of the selected ligand(s) as capped
sticks. The highest scoring pose is displayed for each
selected ligand.
Table When this radio button is active a selection in the list
opens the spreadsheet of poses associated with each
selected ligand. To close an open spreadsheet, simply
unselect the corresponding line in the results list. This
synchronizes the display status in the dialog with what
is on the screen.
Results List
All column headers above the list can be used to sort the entire results list in
either direction. Move any of the vertical bars to adjust the width of the corre-
sponding columns.
E An asterisk flags the single ligand being examined via

the buttons.
M Sort by marked (+) compounds.
Molecule Sort the ligands alphabetically by name.
Score Values Sort by score value. By default, the Total Score values
are sorted from best to worst: decreasing values for
Surflex-Dock.
For details of score values refer to Surflex-Dock Values
in the Results Browser on page 63.
Ligand List The individual ligands are listed, along with the score
of the top scoring pose. Long names may appear trun-
cated in the list. The visible portion of the sorted list is
determined by the Ligand Index and Max Listed
sliders.

Selection Buttons
Buttons to assist in selecting items in the visible list:

select all, invert selection, clear selection. Compounds
already selected, but not in the visible portion of the
list, are not affected.
Select all marked ligands in the visible portion of the
list. See Marking Buttons below.
Examine Controls
Examine compounds one at a time. Multiple poses of the examined ligand can
be displayed. An asterisk identifies the compound in the list.
Move to the previous or to the next ligand (in the visi-

ble portion of the list) and display it. An asterisk flags
this ligand in the results list.
Clear the screen of the ligand that was being examined
and remove the associated asterisk from the list.
If sorting the list moves the examined ligand outside
the visible portion of the list, the ligand is cleared from
the screen and the associated asterisk is also cleared.
Examine N Move the slider to the right to display an increasing
Poses number of poses for that ligand. The maximum number
of poses per ligand is specified at run time. Fewer than
the maximum number of poses may actually be found
for any of the ligands.
The ability to view multiple poses is available only for
the Base score set.
Color Scheme The color of the compound being examined depends on
other factors. See Customizing the Rendering and Col-
ors of Displayed Results on page 62. By default:
• By atom types if the visible list does not include
any selected compounds (compounds may have
been selected in invisible portions of the list).
• Red if any compound is selected in the visible list.
• Green if any compound is selected in the visible list
and if the examined compound is already marked.
Marking Buttons
Marked compounds are flagged with a plus sign (+) in front of their name in the
list. Marking is retained even for compounds that are not in the currently visible
list.

Mark or unmark the ligand being examined.
Clear all marked ligands.
Mark the selected ligand(s).
Workflow:
1. With the Molecule radio button active, mark the compounds of interest
using any combination of the following:
• Select any number of compounds in the list to display them and click
to mark them.
• Use to examine compounds one at a time and click to
mark any you find interesting as you go.
2. Click to clear the selection.
3. Click to select all marked ligands in the visible portion of the list.
4. Switch to the Table view above the list.
5. Click again to open the spreadsheets associated with the ligands
marked in the visible portion of the list.
6. When you are done with the spreadsheets, make sure that the view is set to
Table then click to close them all.
Counters
Tot Total number of successfully docked ligands.

Pos Position of the ligand being examined (flagged with an
asterisk) in the total results list as currently sorted.
Note that only ligands in the visible portion of the list
may be examined.
You may type a number in the text field to examine the
corresponding ligand. However, if you type a number
outside of the visible portion of the list, this field will
be automatically reset to either the first or last ligand in
the visible list, and the corresponding ligand will be
displayed.
Sel Number of selected (highlighted) ligands in the visible
portion of the results list.
Mrk Number of marked ligands in the complete list.

Visualization and Output
Visualization Access the Visualization Options dialog to quickly dis-

play molecular volumes.
Failed Ligands This button is active if the run fails to dock or align one
or more ligands. Press it to access the Failed Ligands
dialog. A copy of the list of failed ligands is saved in
the file jobname_fail.hlpr.
Save Results Access the Saving Results dialog where you can spec-
ify the output format(s) and designate which ligands to
save.
Customizing the Rendering and Colors of Displayed Results
The colors and rendering used to display results via the Results Browser can be
customized through the use of variables.
Example of use: By default, the Results Browser displays molecules with

capped sticks rendering. To disable rendering and display the molecules as
antialiased lines use the following command:
SETVAR FLXANS!RENDERMODE ANTIALIASED_LINES
You may set any of the variables described below in the console (even while the
Results Browser is open). To load your preferences automatically at SYBYL
startup, enter the corresponding lines in your $HOME/sybyl.ini file (sample
sybyl.ini file in the Toolkit Utilities Manual). Any variable not explicitly set
before the first launch of the Results Browser will be set to its default value.
Rendering
You may set the following variables to any of the standard rendering options:
BALLS_ONLY, BALL_AND_STICKS, CAPPED_STICKS (default), SPACEFILL,
STICKS_ONLY. To disable rendering and display the molecules as lines, set the
variable(s) to the single character A (short for ANTIALIASED_LINES).
• FLXANS!RENDERMODE — Used for rendering the displayed molecules.
Default is capped_sticks.
• FLXANS!EXRENDERMODE — Used for rendering the poses of the
examined molecule.
Default is capped_sticks.
Example: setvar flxans!rendermode a

Color of Examined Ligand

The following variables apply only to the color of the ligand being examined
(and its user-specified number of poses) if another ligand is already selected in
the list.
Examined Examined Variable Defining the Default

Ligand is Ligand is Examined Ligand’s Color Color
Selected Marked
Y Y FLXANS!EXAMINECOLOR1 GREEN
N Y FLXANS!EXAMINECOLOR2 GREEN
Y N FLXANS!EXAMINECOLOR3 RED
N N FLXANS!EXAMINECOLOR4 RED
You may set these variables to any of the 24 SYBYL colors (see the Color
Editor in the SYBYL Reference Guide) or to ORIGINAL_COLOR, which by
default is by atom type.
If no other ligands are displayed, the color of the examined ligand is always set
to ORIGINAL_COLOR (which defaults to atom type coloring).
3.2.2 Surflex-Dock Values in the Results Browser

In the Results Browser, the ligand list is automatically sorted by decreasing
value of the total Surflex-Dock score.
The list itself reports the values for the top-scoring pose for each ligand.
To access the information about additional docked poses click Table above the
list then select a ligand in the list. A spreadsheet will open in which each row is
the structure of a docked pose for that ligand.
For a simple Surflex-Dock run the columns contain the following information:
• Total_Score = The total Surflex-Dock score expressed as -log(Kd).
(See The Surflex-Dock Scoring Function on page 79.) The total score
includes the Crash score [Ref. 3].
• Crash = The degree of inappropriate penetration by the ligand into the
protein and of interpenetration (self-clash) between ligand atoms that are
separated by rotatable bonds. Crash scores close to 0 are favorable.
Negative numbers indicate penetration. The smaller the crash score, the
better Surflex-Dock is at screening out false positives. However, this
may discard true positives that fit tightly in the pocket.

• Polar = Contribution of the polar interactions to the total score. The

polar score may be useful for excluding docking results that make no
hydrogen bonds.
If you specified the structure of the known ligand as reference, you will see an
additional column:
• Similarity = Surflex-Sim similarity [Ref. 11] between the top scoring
pose and the ligand provided as a reference for the Surflex-Dock run.
If placed fragment(s) were used to direct the run you will see additional
columns:
• FragIndex = ID number of the fragment that most closely matches the
docked ligand. The ID number reflects the position of the fragment in
the xxx-frag.mol2 file used in the docking run.
• FragRMSD = RMS distance between the docked ligand and the
reported fragment.
If you allowed protein movement, another set of scores is available via the
Score pull-down above the list: Protein Flexibility [PF-re]. The list is repop-
ulated with new values and the following additions:
• Pose = Indication of which pose in the initial run has the best score
after optimization with protein flexibility.
• Strain = Nominal ligand strain relative to the nearby local minimum in
units of pKd.
• Total = Ligand’s score corrected for strain energy.
• Ligmin = Energy of the nearby ligand minimum (kcal/mol).
• Full = Absolute energy of the optimized ligand including protein inter-
action (kcal/mol).
• Complex = Absolute energy of the complex including ligand, protein
pocket, and intermolecular interactions (kcal/mol).
• Cscale = Scaled complex score that normalizes the protein score
components so that ligand poses that contact different numbers of
protein atoms are more directly comparable.
• Pmove = Average movement of the protein atoms in the pocket for this
pose.
If a CScore calculation was performed at the end of the run you will see
additional columns. These are accessible only in the ligand spreadsheets and
they are computed only for the Base score set.
• x_Score = one column for each requested scoring function.

• CSCORE = the consensus score computed from the Surflex-Dock Total

Score and the additional scoring functions.
• GLOBAL_CSCORE = The consensus score across the entire dataset
(for Multi-Mol2 runs only).
3.2.3 View Surflex-Dock Fragment Constraints

Display the fragments used to constraint a Surflex-Dock run.

In the Results Browser, press Constraints.
Fragment List List of all the placed fragments submitted to the dock-
ing run (jobname-constraints.mol2 in the job direc-
tory). Fragments selected in the list are displayed in
capped sticks.
Buttons Navigation and selection buttons to assist in the selec-
tion and display of constraining fragments.
Fragment Color Specify the color style for the displayed fragments. The
Spectrum scheme is particularly useful when includ-
ing multiple fragments in the display of the docking
results.
3.2.4 Visualization Options

Easy display of molecular volumes.
For docking jobs, select:


In the Results Browser press Visualize.
For similarity jobs, select:

Applications > Similarity Suite > Analyze Results
In the Results Browser press Visualize.
MOLCAD Displays the MOLCAD Surfaces dialog and places the

displayed ligands in the dialog’s list of molecules.
Read about MOLCAD Surfaces and license require-
ment in the MOLCAD Manual.
Multi-Volume Surface
The surface style is determined by Tailor variable CONTOUR DISPLAY_AS.
Union Displays, as a green surface, the volume occupied by

the union of the visibly selected ligands. The surface is
displayed as an independent background image in D1.
Intersection Displays, as a yellow surface, the volume shared by all
visibly selected ligands. The surface is displayed as an
independent background image in D1.
Advanced Access the Advanced MVolume Expression dialog to use
more complex expressions to define the volume. This
dialog provides a graphical interface to the MVOLUME
command.
Delete Deletes all the image(s) displayed by the Union and
Intersection buttons and by the Advanced expression.

Hydrogens
Display H-bonds Toggle this check box to turn on and off the display of
H-bonds between displayed site and ligand(s). This fea-
ture is useful when examining docking results. It uses
the Monitor Hydrogen Bonds functionality described in
the Graphics Manual.
Display Toggle this check box to turn on and off the display of
Non-Polar H non-polar hydrogens. By default (off), only polar
hydrogens (those connected to potential H-bond accep-
tors or donors) are displayed.
Topomer Search
Display Query Available for Topomer Search results. Toggle this

check box to turn on and off the display of the query.
By default (on) the query is displayed in yellow.
Advanced Multi-Volume Expression
Display, as a surface, the logical combination of molecular volumes.
Access:
In the Results Browser press Visualization.
In the Visualization Options dialog, press Advanced.
This dialog provides a graphical interface to the MVOLUME command.
List The list is populated by all the ligands visibly selected


Expression Tools Click the buttons and select molecule areas from the list
to form an expression in the field below. Alternatively,
you can type the expression directly into the field.
Briefly, the buttons are:
• ( ) Open and close parentheses for grouping objects
and operations.
• + Union
• - Difference
• & Intersection
• ` Negation
• Del to remove the last button selection from the
expression.
• Clr to clear the entire expression field.
Volume Color Select the color for the resulting volume surface.
OK The surface is displayed as an independent background
in D1 and may be deleted via the Delete button in the
Visualization Options dialog. The surface’s style is
determined by Tailor variable CONTOUR DISPLAY_AS.
3.2.5 View Failed Ligands

List all ligands that failed the docking or alignment procedure.

In the Results Browser press Failed Ligands.

In the Results Browser press Failed Ligands.

Buttons to assist in selecting failed ligands: select all,

invert selection, clear selection. At least one ligand must
be selected for the action buttons below the list to be
active.
Show 2D Struc- Access the SLN 2D Viewer to display a flat representa-
tures tion of the ligands that did not meet the similarity crite-
ria.
Write SLN File Store the selected failed ligands in a 3D SLN file with
the specified Filename.
3.2.6 Save Specified Results

Save the specified number of ligands, and poses for each, in a variety of
formats.

In the Results Browser press Save Results.

In the Results Browser press Save Results.

Save Mode
Mode Specify how to identify the ligands to be saved.

• Score—The type of value to use (when more than
one is available) is specified by Criteria.
• Input Order—The order in the input file.
• Selected—Ligands selected (highlighted) in the
Results Browser.
• Marked—Ligands marked (with a + sign) in the
Results Browser.
Criteria Choose the type of value that will be used to sort the
ligands. The headers for all the value columns in the
Results Browser are listed here.
Order Descending or Ascending—How to sort the ligands
based on the choice made in the Criteria pull-down.
Number of Ligands and Poses to Save
First N Use the slider to specify the number ligands to save.

Number of Available for Surflex-Dock and Surflex-Sim results.
Poses per Use the slider to specify the number of poses to include
Ligand in the output file for each saved ligand.
Strip Pose Pose names consist of the ligand’s name followed by _
Number from xxx where _000 is the top scoring pose. When saving a
Molecule Name single pose per ligand you may want to remove the
pose number from the molecule name. This option is
not available when saving multiple poses per ligand.
Append Pose Include a field or column with the pose number when
Column saving results in SLN, SD, and spreadsheet file formats.
Output
Output Formats Select one or more format(s) for the saved compounds:
• MDB—A SYBYL database of individual .mol2
files.
• SLN File—A file in SLN format (.sln) that includes
all the scores.
• SD File—A file in MDL data format (.sdf) that
includes all the scores.
• Multi-Mol2—A single .mol2 file containing all the
saved compounds.
• Spreadsheet—A spreadsheet of the selected
compounds with their scores. The corresponding
table file (.tbl) is created automatically.

Output Prefix The text string to use to name the file(s) containing the
saved results. The files will be created in the current
working directory.
This text string must start with an alphabetic character
and may contain digits and underscores (_) in any posi-
tion after the first. All other characters will be ignored.
Handling of CScore Results

If CScore results are detected in a docking run, they are saved, and a consensus
score is calculated accordingly. The score and consensus scores can be saved
only to the SLN, SD, and spreadsheet file formats.
Consensus scores are calculated as follows:

• CSCORE computed from Total Score, ChemScore, G-Score, D-Score,
and PMF-Score
• CSCORER (relaxed) computed from ChemScoreR, GR-Score,
DR-Score, and PMFR-Score

3.2.7 The Surflex-Dock Files

After a Surflex-Dock run you will find the following files in the job directory
(jobname).
jobname Surflex-Dock output file.

jobname.file_names List of file names. One of these is job-
name.mol2, containing the ligands to be
docked. If placed fragments are used to con-
strain the run jobname-constraints.mol2 is
also included.
jobname.ligandlist Names of all input ligands in input order.
jobname.log.x Standard output text file(s) produced by Sur-
flex-Dock. A separate file (.x) is produced
for each processor.
The software version is reported as Surflex-
Dock vn.nnn.mmm where n.nnn is provided
by the author and mmm is a Tripos internal
number.
jobname.mol2 Multi-Mol2 file of all input ligands.
jobname_site.mol2 Active site for display in the Results
Browser.
Note: The site file is not used during the run,
but is created as a visual aid when viewing
results. The residues in this file are identi-
fied as those containing at least one atom
within 2.5 Å of any protomol atom. As such,
residues in this file may be different from
those in the user-defined site that may have
been used to generate the protomol.
jobname-constraints.mol2 Multi-Mol2 file of placed fragments if any
were used to constrain the docking run.
jobname-results.mol2 Multi-Mol2 file of docked poses for all
ligands
jobname-results.sln SLN file of docked poses with all computed
scores for all ligands.
jobname-results_tab.log Text file containing all computed scores for
all docked poses.
ligand.tbl Spreadsheet of poses and scores for the
ligand; created upon request in the Results
Browser.
protein-prefix-protomol.mol2 Protomol where prefix reflects the method
used to generate the protomol

protein-prefix.sfxc Surflex-Dock control file where prefix

reflects the method used to generate the pro-
tomol
protein_H.mol2 Prepared receptor file
Docking Run with Protein Flexibility

In the Surflex-Dock - Details dialog activate Allow Protein Movement.
jobname-PF-re Surflex-Dock output file produced by the

optimization (rescoring) step of a docking
run.
jobname-PF-re-merged.mol2 Multi-Mol2 file of merged protein-ligand
poses.
jobname-PF-re-protein- Multi-Mol2 file of protein poses associated
results.mol2 with all the ligand docked poses.
jobname-PF-re-protein- SLN file of protein poses associated with all
results.sln the ligand docked poses.
jobname-PF-re-results.mol2 Multi-Mol2 file of optimized docked poses
for all ligands.
jobname-PF-re-results.sln SLN file of optimized poses with all com-
puted scores for all ligands.
jobname-PF-re-results_tab.log Text file containing all computed scores for
all optimized poses for all ligands.
Helper Files
._fail.hlpr Text file created by the Results Browser.

._orig.hlpr Text file created by the Results Browser.
._proclog.hlpr Text file created by the Results Browser.
._sort.hlpr Text file created by the Results Browser.
.enginemode SurflexDock
.split Directory containing a Mol2 file for each of
the input ligands
CScore
CScore Directory of .cso files, one per ligand. Each

file contains the CScore values for all
docked poses.
cscore.file_names File containing the jobname.

cscore.par Copy of the CScore parameter file used in

the docking run. By default $TA_MOLTA-
BLES/cscore.par unless another file has
been specified via Tailor variable CSCORE
PARAMETER_FILE.
CScoreOutputLocation Full path to the CScore directory.
protein_H.pmf Copies of protein_H.mol2 with appropriate
protein_H.gld extensions for each of the scoring functions
protein_H.chm in CScore.

4. Surflex-Dock

dock ligands into a protein’s binding site. Docking is guided by the protomol,
an idealized representation of a ligand that makes every potential interaction
with the binding site. The protomol can be generated automatically or defined
based on a cognate ligand or known active site.
Surflex-Dock is particularly successful at eliminating false positive results and

can, therefore, be used to narrow down the screening pool significantly, while
still retaining a large number of active compounds.
• Run Surflex-Dock Standalone on page 76
• Surflex-Dock on a Local Network on page 76
• Surflex-Dock on a Commercial Queuing System on page 76
• The Surflex-Dock Method on page 77
• The Surflex-Dock Protomol on page 77
• The Surflex-Dock Docking Procedure on page 78
• The Surflex-Dock Scoring Function on page 79
• Ligand Preparation for Surflex-Dock on page 80
• Recommended Reading about Surflex-Dock on page 80
Acknowledgments

4. Surflex-Dock
Run Surflex-Dock Standalone
4.1 Run Surflex-Dock Standalone

Surflex-Dock as distributed with SYBYL may be used in standalone mode.
Licensing:
License Requirements for the Docking Suite on page 7.
Access:
1. Open a system shell with the SYBYL environment.
! Refer to SYBYL-X Environment Shell in the SYBYL Basics Manual.
2. Select where to submit the job.

• Surflex-Dock on a Local Network
• Surflex-Dock on a Commercial Queuing System
4.1.1 Surflex-Dock on a Local Network

Syntax:
$TA_BIN/surflex-dock.exe
Documentation:
BioPharmics’ Surflex Manual.
4.1.2 Surflex-Dock on a Commercial Queuing System

Supported Queueing Systems:
The $TA_ROOT/bin/unix/surflex-dock_cluster.sh script handles the distri-

bution of Surflex-Dock jobs to the following systems supported on Linux:
• Torque/Maui grid
• Oracle Grid Engine
(http://www.oracle.com/technetwork/oem/grid-engine-166852.html)

4. Surflex-Dock
The Surflex-Dock Method
4.2 The Surflex-Dock Method

4.2.1 Introduction

dock ligands into a protein’s binding site. It is particularly successful at elimi-
nating false positive results and can, therefore, be used to narrow down the
screening pool significantly, while still retaining a large number of active
compounds.
The Surflex-Dock method is described in Jain, A.N. “Surflex: Fully Automatic

Flexible Molecular Docking Using a Molecular Similarity-Based Search
Engine.” J. Med. Chem. 2003, 46, 499-511.
4.2.2 The Surflex-Dock Protomol

The Surflex-Dock protomol is a computational representation of the intended
binding site to which putative ligands are aligned.
The protomol is not meant to be an absolute docking envelope. Its purpose is to

direct the initial placement of the ligand during the docking process. Docked
ligands are scored in the context of the receptor, not in the context of the
protomol.
Surflex-Dock constructs the protomol in the following manner.

1. The protein’s surface is coated with three types of probes that represent
potential hydrogen bonds and favorable hydrophobic interactions with
protein atoms.
• CH4 is the steric, hydrophobic probe (H in Surflex-Dock releases prior
to 2.0).
• N-H is the hydrogen bond donor probe.
• C=O is the hydrogen bond acceptor probe.
2. A scoring function (below and Ref. 7) positions and orients the probes to
optimize their interactions with the protein atoms. Each probe’s score repre-
sents the binding contribution of a similar atom on a ligand.
3. Only the probes with the best scores are kept. Spatially redundant and
isolated probes are pruned. The atom density of the remaining set of probes
is similar to that of a potential ligand, the density being slightly higher in
regions where different hydrogen bonds can be made with the protein.

4. Surflex-Dock
4. Given that each probe’s score represents that probe’s contribution to the
protein-ligand binding affinity, clusters of high scoring probes identify the
“stickiest” parts of the protein’s surface. The algorithm searching for sticky
spots is biased toward hydrophobic regions in the interior of the protein
because many protein-ligand complexes involve a receptor pocket, and the
binding affinity is often due in large part to hydrophobic interactions.
5. Before regrouping the sticky spots into a pocket, it is necessary to eliminate
disconnected sticky spots, thereby avoiding disconnected pockets. Spheres
are placed on a 1 Å cubical grid. Each sphere grows until it reaches the van
der Waals surface of a protein atom. Spheres with radii less than 0.5 Å are
discarded. The remaining set of protein-free spheres approximates a
negative image of the protein.
6. The sticky spots are merged into a pocket, the protomol, through a process
of accretion on the set of protein-free spheres. The final dimension of the
protomol is biased toward a size that can accommodate a small ligand.
Surflex-Dock’s protomol building method is described in Ruppert, J.; Welch,

W.; Jain, A.N. “Automatic identification and representation of protein binding
sites for molecular docking.” Protein Sci. 1997, 6, 524-33.
4.2.3 The Surflex-Dock Docking Procedure

Input to Surflex-Dock consists of:
• The 3D structure of a receptor protein with hydrogens and binding site
empty of co-crystallized ligand (if any).
• The protomol, a set of probes (CH4, N-H, C=O) complementary to the
active site (see The Surflex-Dock Protomol above).
• 3D ligands, properly typed, with hydrogens, and in any arbitrary
optimized conformation.
For each ligand rotatable bonds are identified as all single or amide, acyclic,
non-terminal bonds. Surflex-Dock’s treatment of ring flexibility is optional and
uses a small, generic library of 5, 6, or 7-membered rings.

4. Surflex-Dock
4.2.4 The Surflex-Dock Scoring Function

Surflex-Dock uses an empirically derived scoring function that is based on the
binding affinities of protein-ligand complexes and on their X-ray structures.
The Surflex-Dock scoring function is a weighted sum of non-linear functions

involving van der Waals surface distances between the appropriate pairs of
exposed protein and ligand atoms.
The list of atom pairs of interest is established by pruning out all protein-ligand
atom pairs for which the distance between their van der Waals surfaces is
greater than 2 Å. Each atom in the remaining protein-ligand pairs is labeled as
being non-polar (e.g. H in CH3) or polar (e.g. H in N-H or O in C=O). Each
polar atom is also assigned a charge.
The scoring function includes the following terms:

• Hydrophobic—A weighted sum over all atom pairs, in which at least one
atom is non-polar, of functions capturing the positive atomic contacts
and the atomic interpenetration.
• Polar—A sum over all pairs of complementary polar atoms of a function
capturing the effects of hydrogen bonds and salt bridges. This function
includes a directionality term that favors hydrogen bonding geometries
observed in crystal structures and a term that accounts for favorable
interactions between formally charged atoms (if present).
• Repulsive—A sum over all pairs of polar atoms that are of the same sign.
This function captures unfavorable polar contacts.
• Entropic—A function that models the loss of translational and rotational
entropy of the ligand once it is docked. This function takes into account
the number of rotatable ligand bonds and the ligand’s molecular weight.
• Solvation—A function that captures the difference between the potential
and actual numbers of hydrogen bond equivalents.
• Crash—The degree of inappropriate penetration into the protein by the
ligand as well as the degree of internal self-clashing that the ligand is
experiencing. Crash scores that are close to 0.0 are favorable.
Surflex-Dock scores are expressed in -log10(Kd) units to represent binding

affinities.
The Surflex-Dock scoring function and the protein-ligand complexes used to

calibrate it are described in Jain, A.N. “Scoring noncovalent protein-ligand
interactions: A continuous differentiable function tuned to compute binding
affinities.” J. Comput. Aided-Mol. Des. 1996, 10, 427-40.

4. Surflex-Dock
4.2.5 Ligand Preparation for Surflex-Dock
Aromatic vs. Kekule

Surflex-Dock results are dependent upon having a properly typed input ligand.
However, certain functional groups may be typed in more than one manner (as
is the case for aromatic vs. Kékulé), leading to potentially different results. For
example, a carboxylate group (RCOO-) may be typed in aromatic form as two
equivalent aromatic bonds, or in Kékulé form as one single bond and one
double bond. The two descriptions have different electrostatic arrangements,
and subsequently may (or may not) produce different results. Whenever you are
presented with this situation, Tripos recommends using the aromatic form of the
functional group.
Atomic Charges
Surflex-Dock does not use atomic charges. Atoms are assigned to be polar or
non-polar. Polar atoms are assigned a “charge” that reflects their hydrogen bond
ability.
Example of Surflex-Dock charge values:

• Oxygen: 0.500
• Chlorine: -1.750
A positive magnitude indicates a stronger than H-bond charge (whether for a

negative or positive moiety). A negative magnitude makes a weak acceptor (e.g.
a chloride or certain sulfurs).
It is, therefore, very important to pass Surflex the molecules in the protonation
state you think is relevant at biological pH, including non-polar hydrogens.
4.2.6 Recommended Reading about Surflex-Dock

[1] Jain, A.N. “Surflex-Dock 2.1: Robust Performance from Ligand
Energetic Modeling, Ring Flexibility, and Knowledge-Based Search”
J. Computer-Aided Molecular Design. 2007, 21, 281-306.
[2] Jain, A.N. “Effects of protein conformation in docking: improved pose
prediction through protein pocket adaptation” J. Comput. Aided. Mol.
Des. 2009, 23, 1573-4951.
[3] Pham, T.A.; Jain, A.J. “Parameter Estimation for Scoring Protein-Ligand
Interactions Using Negative Training Data” J. Med. Chem. 2006, 49,
5856-5868.
[4] Jain, A.N. “Virtual screening in lead discovery and optimization”
Current Opinion in Drug Discovery & Development 2004, 7, 396-403.

4. Surflex-Dock
[5] Jain, A.N. “Surflex: Fully Automatic Flexible Molecular Docking Using
a Molecular Similarity-Based Search Engine” J. Med. Chem. 2003, 46,
499-511.
[6] Ruppert, J.; Welch, W.; Jain, A.N. “Automatic identification and
representation of protein binding sites for molecular docking” Protein
Sci. 1997, 6, 524-33.
[7] Jain, A.N. “Scoring noncovalent protein-ligand interactions: A
continuous differentiable function tuned to compute binding affinities”
J. Comput. Aided Mol. Des. 1996, 10, 427-40.
[8] Kellenberger, E.; Rodrigo, J.; Muller, P.; Rognan, D. “Comparative
Evaluation of Eight Docking Tools for Docking and Virtual Screening
Accuracy” PROTEINS: Structure, Function, and Bioinformatics 2004,
57, 225-242.
[9] Krier, M.; de Araújo-Júnior, J.X.; Schmitt, M.; Duranton, J.; Justiano-
Basaran, H.; Lugnier, C.; Bourguignon, J-J.; Rognan, D. “Design of
Small-Sized Libraries by Combinatorial Assembly of Linkers and
Functional Groups to a Given Scaffold: Application to the Structure-
Based Optimization of a Phosphodiesterase 4 Inhibitor” J. Med. Chem.
2005, 48, 3816-3822.
[10] Bissantz, C.; Folkers, G.; Rognan, D. “Protein-based virtual screening of
chemical databases. 1. Evaluation of different docking/scoring
combinations” J. Med. Chem. 2000, 43, 4759-4767.
[11] Jain, A. N. “Morphological similarity: A 3D molecular similarity
method correlated with protein-ligand recognition” J. Comp.-Aided Mol.
Des., 14, 199-213 (2000).
[12] More publications at: http://www.biopharmics.com/publications.html
[13] BioPharmics’ Surflex Manual: Docking and Similarity.

This page intentionally blank.
Docking Suite Index
A M
Active site MOLCAD
defining 40 channels
to find active site 37
B
Bibliography
P
Surflex-Dock 80 Protomol 77
generate 37
C
Concord
R
3D coordinate generation References
Surflex-Dock 48 Surflex-Dock 80
Constraints Results
Surflex-Dock placed fragments 42 saving 69
CScore Results Browser 56
details 54 customizing 62
D S
Docking Saving
CScore details 54 docking results 69
dialogs 31 similarity results 69
files created Similarity
Surflex-Dock 72 save results 69
introduction 5
main dialog 32 Suggested reading
results browser 56 Surflex-Dock 80
save results 69 Surflex-Dock 75
Surflex-Dock 75 active site creation 40
docking procedure 78 atomic charges 80
references 80 charges 80
scoring function 79 columns in the results browser 63
tutorials 9 command line 76
theory details 47
Surflex-Dock 77 docking procedure 78
tutorials files created 72
Surflex-Dock 9 graphical user interface 31
introduction 5
license requirements 7
F ligand preparation 80
Files created protein flexibility 48
Surflex-Dock 72 protomol 77
references 80
results browser 56
L runtime parameters 53
License requirements scoring function 79
Docking 7 substructure removal 39
Surflex-Dock 7 theory 77
tutorial 9

T
Topomer Search
query display 67
U
UIMS variables
results browser 62
V
Variables
results browser 62
Visualization options 65

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Docking Suite Manual

1699 South Hanley Rd. Phone: +1.314.647.1099

1. Introduction to the Docking Suite . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

3. Using the Docking Suite . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31

SYBYL-X 2.1 Docking Suite 3

SYBYL provides a graphical interface to Surflex-Dock.

Surflex-Dock uses an empirical scoring function and a patented search engine to

Surflex-Dock is particularly successful at eliminating false positive results and

SYBYL-X 2.1 Docking Suite 5

1.1 What is New with the Docking Suite

With the changes in Surflex, the Surflex-Dock and Surflex-Dock Screen

SYBYL’s interface to Surflex-Dock includes a new feature to identify the

New Job Submission Options

Defining Protomol by Residues

Surflex-Dock Customize Scoring Function

Timing for Protomol Generation

6 Docking Suite SYBYL-X 2.1

1.2 License Requirements for the Docking Suite

1.2.1 Surflex-Dock Licensing

SYBYL-X introduced a simplified licensing scheme:

Access to the Surflex-Dock functionality requires the following licenses:

To submit a Surflex-Dock job SurflexDock and SurflexDock_Interface

Additional features are accessible through the SYBYL interface to Surflex-

Generate 3D coordinates ConcordStandalone

SYBYL-X 2.1 Docking Suite 7

Consensus scoring CScore—For fast CScore processing

1.2.2 License Requirements for the Docking Tutorials

8 Docking Suite SYBYL-X 2.1

Licensing: See License Requirements for the Docking Suite on page 7.

Platform Note: Differences in mathematical rounding on different platforms

SYBYL-X 2.1 Docking Suite 9

2.1 Perform a Simple Surflex-Dock Run

! > Delete Everything

! Click to reset all rotations and translations.

! Type: cmd cp $TA_DEMO/surflex/1kim.pdb . (Include the space

2.1.2 Access Surflex-Dock and Prepare the Protein

! Applications > Docking Suite > Dock Ligands

The Docking dialog is displayed (dialog description on page 32).

! Set the Docking Mode to Surflex-Dock Screen (SFXC) and press

The Surflex-Dock -Define SFXC File dialog is displayed (dialog description on

4. Read in the protein.

! In the Surflex-Dock -Define SFXC File dialog set the Protein

10 Docking Suite SYBYL-X 2.1

5. Start the protein preparation.

The Prepare Protein Structure dialog is displayed (dialog description in the

The Select Substructures dialog is posted.

! In the Substructures field, type B/* and press Apply.

! In the Other list, click on A/SO4_3 to add it to the selection.

! Press (Select All) to the right of the Water list.

All of the water molecules are selected.

! Press OK to delete all selected items.

SYBYL-X 2.1 Docking Suite 11

7. Identify the ligand to be extracted from the cavity.

! Press Extract Ligand Substructures.

! In the Select Substructures dialog click on A/THM1.

! Click OK to accept the selection.

8. Analyze the protein structure and prepare it for docking.

The analysis revealed problems with a few residues.

! Press the Show buttons associated with Repair Backbone, Repair

! In the Add Hydrogens dialog click OK to add all the hydrogens.

12 Docking Suite SYBYL-X 2.1

! Press Fix next to Type Atoms.

The amount of minimization to perform is a matter personal preference and