Docking MD

An introduction into
“Docking”
and
“Molecular Dynamics simulations”
Univ. Ass. Dipl.-Ing. (FH) Dr. scient. med. Bernhard Knapp

Center for Medical Statistics, Informatics and Intelligent Systems
Department for Biosimulation and Bioinformatics
Medical University of Vienna / AKH (General Hospital)
bernhard.knapp@meduniwien.ac.at
23.02.2012 Bernhard Knapp 1
TOC
1. Basic biology knowledge

2. Docking
• Docking in general
• Example AutoDock
3. Molecular Dynamics
• Introduction
• Limitations
• Example Gromacs
3. Tutorial on PDB / jmol

Basic biology knowledge
Amino acids
Build up proteins (german “Eiweiß”)

all have the same basic structure (“backbone” consisting of an amine
group, a carboxylic acid group and a C-alpha atom) but differ in their
side-chain => residue (the side chain defines which AA it is)
20 different canonical amino acids (AAs) are existing (that means 20

different side-chains)
23.02.2012 4
Wikimedia
Wikimedia
23.02.2012 5
Several amino acids are connected via „peptide bonds“
Wikimedia

Then they are called:
peptide: > 1 AA
oligopeptide: < 10 (other sources state 30)
polypeptide: > 10 AAs
protein: > 50 AAs
macropeptide: > 100 AAs
monopeptide: 1 AA
dipeptide: 2 AA
tripeptide: 3 AA
tetrapeptide: 4 AA
pentapeptide: 5 AA
hexapeptide: 6 AA
heptapentide: 7 AA
octapeptide: 8 AA
nonapeptide: 9 AA
decapeptide: 10 AA
undecapeptide: 11 AAs
...
icosapeptide: 20 AAs
tricontapeptide: 30 AAs
tetracontapeptide: 40 AAs
… however the exact definitions differ (and you do not need to learn them for
the examination of this lecture!)
Structure levels
Primary structure: the pure sequence of the AAs
Secondary structure: e.g. beta-sheet, alpha-helix, or turns
Tertiary structure: 3D arrangement of secondary structure

elements
Quaternary structure: several proteins together
Wikimedia

How we can illustrate them
(also see the tutorial at the end)
23.02.2012 9
And what
about the
size of
proteins
and AAs?
[Janeway]
~20x20x20 nm ~13x6x5 nm
1 Nanometer == 10-9m == 0.0000000001m
2 more definitions:
Ligand: also known as (small) peptide, epitope, guest, antigenic

determinant
Receptor: also known as (big) protein, host, macro molecule

Docking in general
What does docking mean?
trying to find the „best matching“ between 2 molecules

Who could fit to me?
/ / / / .
Let us try with this one …
- („induced fit“)
23.02.2012 15

[Kitchen et al., 2004]
Why is docking useful?
Docking (~Virtual Screening) is of paramount interest for drug discovery

For one target millions of different possible drugs can be tested
The best n matches will be tried in experiments
Will save time, resources and money

Usually 3 steps
1) Decide how to search through the spatial space
2) Decide how flexible ligand and receptor can be
3) Decide how to score various parameter sets
Where is the difficulty?
1) 6 degrees of freedom in 3d space (3 translational, 3 rotational)

2) 100+ degrees of freedom if we consider full flexibility of all bounds
3) nearly each atom interacts witch every other one
23.02.2012 Bernhard
B h d Knapp
K 20
Ad 1) Search Algorithms used (for spatial space)
Systematic docking
- Brute Force
- Fragmentation
- Database
Heuristic docking
- Monte Carlo
- Genetic algorithms
- Tabu search
Simulations Docking
- Molecular Dynamics
- Gradient (Energy) Methods
Ad 2) Deciding about the flexibility

“rigid body” docking
- receptor and ligand are considered as 100% rigid
- very fast (6dfs only), but inaccurate
“induced fit” docking

- moveable [backbone| side] chains
“flexible ligand”
- only the ligand is considered als flexible, the receptor remains rigid
“full flexibility”
- computational very expensive

Ad 3) Scoring functions (1/2)
Force Field based scoring function

- energy of the interaction and internal energy of the ligand
- combination of : Van der Waales, Lennard Jones, electrostatic energy,
…
- e.g. D-Score, GoldScore, AutoDock, CHARMM, …
empirical scoring functions
- Trying to reproduce experimental observed docking behaviors by
means of formulas
- usually the sum of uncorrelated terms
- e.g. LUDI, F-Score, SCORE, X-SCORE, …
Scoring Funktionen (2/2)
Knowledge based scoring function

- trying the deduce rules form experiments
- e.g. DrugScore, PMF, …
Geometrical scoring function
- based on shape complementarity
- e.g. Connely Surface, Soft Belt Scoring
Consensus scoring function
- hybrid versions
- e.g. various Review Papers: [Trost, 2005]

Difference between position score and rank score
„The pose score is often a rough measure of the fit of a ligand into the
active site. The rank score is generally more complex and might attempt to
estimate binding energies.“
"relatively small chemical modifications can lead to significant changes in

binding."
[Kitchen et al., 2004]
23.02.2012 25
23.02.2012 Bernhard Knapp [Sousa, 2006] 26

23.02.2012 Bernhard Knapp [Sousa, 2006] 27
Correct result vs incorrect result
23.02.2012
223
… and what about the correctness and reliability?
Currently correct results are more or less restricted to the area where the
tools have been calibrated
e.g. for pMHC the area under the ROC is between 0.5 and 0.75 using
different substitution and scoring tools [Knapp, 2008]
But
"We have long known that there is nothing in biology which is
fundamentally inconsistent or incommensurable with mathematics,
chemistry, and physics. Biology long ago rejected vitalism. The only
information needed for life is provided by an organism's chemical
constituents. It is unlikely in the extreme that living systems cannot be
understood in terms of chemistry and physics.“ [Wan, 2008]
Example Autodock

What is Autodock
“AutoDock is a suite of automated docking tools. It is designed to predict

how small molecules, such as substrates or drug candidates, bind to a
receptor of known 3D structure. AutoDock actually consists of two main
programs: AutoDock performs the docking of the ligand to a set of grids
describing the target protein; AutoGrid pre-calculates these grids. In
addition to using them for docking, the atomic affinity grids can be
visualised. This can help, for example, to guide organic synthetic chemists
design better binders.”
url: http://autodock.scripps.edu/
search algorithms used for spatial space

Systematic docking
- Brute Force
- Fragmentation
- Database
Heuristic docking
- Monte Carlo
- Genetic algorithms
- Tabu search
Simulations Docking
- Molecular Dynamics
- Gradient (Energy) Methods

Deciding about the flexibility
“rigid body” docking
- receptor and ligand are considered as 100% rigid
- very fast (6dfs only), but inaccurate
“induced fit” docking

- moveable [backbone| side] chains
“flexible ligand”
- only the ligand is considered als flexible, the receptor remains rigid
“full flexibility”
- computational very expensive
Scoring functions (1/2)
Force Field based scoring function

- energy of the interaction and internal energy of the ligand
- combination of : Van der Waales, Lennard Jones, electrostatic energy,
…
- e.g. D-Score, GoldScore, AutoDock, CHARMM, …
empirical scoring functions
- Trying to reproduce experimental observed docking behaviors by
means of formulas
- ususlly the sum of uncorrelated terms
- e.g. LUDI, F-Score, SCORE, X-SCORE, …

Scoring Funktionen (2/2)
Knowledge based scoring function

- trying the deduce rules form experiments
- e.g. DrugScore, PMF, …
Geometrical scoring function
- based on shape complementarity
- e.g. Connely Surface, Soft Belt Scoring
Consensus scoring function
- hybrid versions
- e.g. various Review Papers: [Trost, 2005]
Autodock: sampling of spatial space (1/4)
Simulated Annealing
Random start up position, e.g. here

Quality of solution
Stack in local min
Global min
Different solutions
simulated annealing (german “abkühlen”) procedure:
Idea: local neighborhood search but „sometimes“ accepting worse

solutions (certain probability)
E j Ei
Similar to annealing of crystals in physics
k BT
1. Melt a solid body in a heating pot p e
2. Atoms are almost randomly distributed
3. Slowly anneal
4. At each temperature a thermical balance is found
5. Atoms will arrange in an energetically advantageous position

Genetic Algorithms
- A set a values is used to define the ligand, receptor and their
current states
- Doing it as nature:
1. Creating random population of solutions P1 P2 C1
2. Evaluation of fitness 24 23 24
3. Selection of the fittest n solutions 46 66 46
78 84 78
4. cross over, mutation, … 90 × 90 90
5. goto 2 again 4 92 92
33 12 12
99 78 5
65 44 44

Autodock: Flexibility (1/1)
receptor hold rigid

ligands bounds have full flexibility according to a rotamer library
state of ligands bounds are represented as genes in the GA
Autodock: Scoring in 1998 (1/1)
12, 6 Lennard Jones

potential
Hydrogen bounds,
weighted by angle t
Electrostatic forces
Torsion angles
Solvation effects

Autodock2007: in general zero!
Autodock2007: unbound?
3 approches for the unbound state
Extended
Compact
Bound

Autodock2007
Autodock2007: the formula
the weighting factors W have been calibrated on a set of 188

recptor/ligand complexes with known experimental binding affinities
Coordinates from the protein data bank (www.pdb.org)
Binding data from ligand-protein database (http://lpdb.scripps.edu/)

Autodock2007: AD3 vs AD4
Autodock2007: successrate against exp data
75 cases: found but other

scored better
67 cases: found and
scored best
28 cases: not found
=> 84% of all ligands found

Video Autodock
[published on Autodock Homepage]
Biologists have often concerns about the success of computational

techniques. [Jorgensen, 2004] nicely summarizes such a situation:
“’Is there really a case where a drug that’s on the market was designed by a
computer?’ When asked this, I invoke the professorial mantra (’All questions
are good questions.’), while sensing that the desired answer is ’no’. Then,
the inquisitor could go back to the lab with the reassurance that his or her
choice to avoid learning about computational chemistry remains wise.”
So what is the role of computers in drug discovery?
23.02.2012 48
Take home messages for the first part
Computational methods can be used to identify potential drugs

They can help to reduce the number of candidates to test or predict a
set of possible candidates. However, they can not predict the one and
only working substance in one step
The methods are diverse
Nowadays there is still much space for improvement of the methods
"The day is coming when theory and computation will guide biology, as
it does physics now.“ [Wan, 2008]
Molecular Dynamics (MD)

Introduction
MD is a type of computer simulation

Atoms interact under given laws of physics for a specified time
MD can be seen as an interface between “wet”-lab experiments and
theoretical models
Used to analyze the spatial and energetic dynamics of e.g. bio-
molecules, materials, …
Usually very computational power and memory consuming
Calculate forces between all atoms of the system …
n=6, usually n>1000
… but what does forces mean?
A combination of bonded and non-bonded interactions …

Bonded interactions
bond length
ே್
1
ܸ௕ = ෍ ‫ܭ‬௕೙ ܾ௡ െ ܾ௡଴ ଶ ܾ௡ = ‫ݎ‬௜௝ = ‫ݎ‬௜ െ ‫ݎ‬௝
2
௡ୀଵ
bond angle
‫ݎ‬௜௝ ή ‫ݎ‬௞௝
ߠ௡ = ܽ‫ݏ݋ܿ ܿݎ‬
‫ݎ‬௜௝ ή ‫ݎ‬௞௝
torision
1
ܸఝ = ‫ ܭ‬1 + ܿ‫݌ ݏ݋‬௡ ߮௡
2 ఝ೙
‫ݎ‬௜௝ × ‫ݎ‬௞௝ ή ‫ݎ‬௞௝ × ‫ݎ‬௞௟
߮௡ = arc cos
‫ݎ‬௜௝ × ‫ݎ‬௞௝ ή ‫ݎ‬௞௝ × ‫ݎ‬௞௟
What does the „bond length“ term really mean?

perfect
too far
away
[Shaw et al.]
too
close
23.02.2012 54
What does the „bond angle“ term really mean?
perfect
too big
[Shaw et al.]
too
small
23.02.2012 55
What does the „torsion“ term really mean?
perfect
tilted
[Shaw et al.]
23.02.2012 56
Non bonded interactions
ே ே
1
ܸே஻ = ෍ ෍ ܸ௜௝௅௃ + ܸ௜௝ா௅
2
௜ ௝
Coulomb
‫ݍ‬௜ ‫ݍ‬௝
ܸ௜௝ா௅ =
‫ݎ‬௜௝
Lennard-Jones
ଵଶ ଺
ߪ௜௝ ߪ௜௝
ܸ௜௝௅௃ = 4߳௜௝ െ
‫ݎ‬௜௝ ‫ݎ‬௜௝
What does the „coulomb“ term really mean?
[Shaw et al.]
23.02.2012 58
What does the „Lennard-Jones“ term really mean?
perfect
too far
away
[Shaw et al.]
too
close
23.02.2012 59
This all together is called a „force field“
… and of course the real implementations are way

more complicated. There are several software
packages available (e.g. GROMACS, AMBER,
CHARMM, Schroedinger, …)
What can we do with this force field?
We divide time into discrete time steps of e.g. 1 fs (= 10-15 s)
0 fs t -> 10 000 000 fs (=10 ns)
… and calculate the forces for each time step while adjusting the postions
Iterate …
and iterate …
and iterate …
and iterate …
and iterate …
Finally we get something like this:
In reality however more like this:
[from wikipedia]
„The equations are solved simultaneously in small time steps. The system is
followed for some time, taking care that the temperature and pressure remain at
the required values, and the coordinates are written to an output file at regular
intervals. The coordinates as a function of time represent a trajectory of the
system.“ [Gromacs Manual]
Flow diagram of a MD:
Define initial atoms positions
Calculate forces
Move atoms
Increment time
Stop criterion
reached?

Example for MD simulation using Gromacs
[Hess et al., 2008]
1. Obtain atom coordinates for the system to be simulated (e.g. pdb

format from www.pdb.org) (takes minutes to days, mostly depended
on the human)
2. Validate the pdb file (takes seconds)
3. Create a virtual simulation box around the system (takes seconds)
4. Fill the box with artificial water (takes seconds)
5. Minimize the energy of the system (takes minutes to hours)
6. Warm the system up to room temperature (takes hours to days)
7. Start the real MD simulation (takes days to months)
8. Evaluate Results (takes minutes to years(!) depended on the human)
Example for MD simulation
0 ns 20 ns

Video MD-Simulation shown via VMD
Example for
MD simulation

Limitations of MD simulations (1 of 2)
(on the basis of Gromacs)
Newton’s equations of motion describe classical mechanics, not

quantum mechanics (=> sometimes problems with e.g. hydrogen
atoms)
Electrons are in ground state: they are supposed to adjust their
dynamics when the atomic positions changes (Born-Oppenheimer
approximation)
Force fields are approximate: balance between computational load and
accuracy, their parameters can be user-modified
Force fields are pair additive: omission of polarization
Limitations of MD simulations (2 of 2)
(on the basis of Gromacs)
Long range interactions are cutoff: only one image of each particle in
the periodic boundary conditions is considered => cutoff can not
exceed half the box size
Boundary conditions are unnatural: a lot of particles have vacuum as
neighbor to avoid that periodic boundary conditions are used.
=> Sometimes the system is influencing itself
Computational costs and runtime (3 months for 20 ns!)
Cumulative errors in numerical integration and limitation in floating
point representation

Evaluations of MD-trajectories
Now we have something like that:
… a huge set of individual configurations over time. But what does this
agglomeration of single structures tell us?
RMSD
First idea: difference of the single frames (transparent) from starting

structure (solid). Calculate the root mean square deviation:
¦ r
N
1 2
RMSD i
X
riY
N i 1
Where N is the number of atoms, i is the current atom, rX is
the target structure and rY is the reference structure.
Be careful if you compare structures with different positions and

rotations in space. You will properly need to superimpose (fit) them first.

RMSD cont
The RMSD over time (in this case rY is the first frame)
All frames:
Frame
with
highest
RMSD:

Radius of Gyration
A similar measurement is the radius of gyration. It measures the

distance of the regions’ parts from its center of gravity.
Or in other words how packed a certain region is.
E.g.
The radius of gyration is an interesting property since it can be

determined experimentally using “static light scattering” as well as with
“small angle neutron-” or “x-ray scattering”. This allows theoretical
scientists to check their models against reality.
RMSF
Next idea: fluctuation of a particular amino acid over time. Calculate the
“root mean square fluctuation”:
M
¦ r (t ri
1
)~
2
RMSFi i k
M k 1
Where M is the number of frames taken into account,

ri(tk) is particle i of complex r at time k and r with tilde
is the reference. This reference can for example be
the average over a given time window.

RMSF cont

SASA
How much of a certain area is exposed to the solvent (e.g. a amino acid
or a region)? Calculate the solvent accessible surface area
solvent
protein
(possible)
target
SASA
Methodology to calculate the SASA:


Take home messages for the second part
MD is a computer simulation of “real” atom-atom interactions

MD is very time and resource consuming
The output trajectories are huge and various ways to analyze them are
existing
There are still certain limitations
Tutorial on PDB / jmol

Introduction TCRpMHC interaction on white board
23.02.2012 87
www.pdb.org => 1mi5

right click => „console“
select *
cartoon off
select *:C
wireframe 100
Opinions, comments und suggestions?

Further literature
Docking:
Sousa SF, Fernades P, Ramos MJ. Protein-Ligand Docking Current Status and Future Challanges, Proteins
2006; 65:15-26.
A semiempirical free energy force field with charge-based desolvation. Huey,R., Morris,G.M., Olson,A.J., and
Goodsell,D.S. (2007). J Comput Chem. 28, 1145-1152.
Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. Morris,
G. M., Goodsell, D. S., Halliday, R. S., Huey, R., Hart, W. E., Belew, R. K., and Olson, A. J. J.Computational
Chemistry 19, 1639-1662. 1998.
Kitchen DB, Decornez H, Furr JR, Bajorath J. Docking and scoring in virtual screening for drug discovery:
methods and applications, Nat. Rev. Drug Discov. 2004; 3:935-949.
Molecular Dynamics simulations:
Dodson GG, Lane DP, Verma CS (2008) Molecular simulations of protein dynamics: new windows on
mechanisms in biology. EMBO Rep 9: 144-150.
Karplus M, Kuriyan J (2005) Molecular dynamics and protein function. Proc Natl Acad Sci U S A 102: 6679-
6685.
Hess B, Kutzner C, vanderSpoel D, Lindahl E. GROMACS 4: Algorithms for Highly Efficient, Load-Balanced,
and Scalable Molecular Simulation. J Chem Theory Comput 2008.

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An introduction into

Univ. Ass. Dipl.-Ing. (FH) Dr. scient. med. Bernhard Knapp

23.02.2012 Bernhard Knapp 1

1. Basic biology knowledge

23.02.2012 Bernhard Knapp 2

23.02.2012 Bernhard Knapp 3

 Build up proteins (german “Eiweiß”)

 20 different canonical amino acids (AAs) are existing (that means 20

Several amino acids are connected via „peptide bonds“

23.02.2012 Bernhard Knapp 6

23.02.2012 Bernhard Knapp 7

 Primary structure: the pure sequence of the AAs

 Secondary structure: e.g. beta-sheet, alpha-helix, or turns

 Tertiary structure: 3D arrangement of secondary structure

 Quaternary structure: several proteins together

23.02.2012 Bernhard Knapp 8

1 Nanometer == 10-9m == 0.0000000001m

 Ligand: also known as (small) peptide, epitope, guest, antigenic

23.02.2012 Bernhard Knapp 12

23.02.2012 Bernhard Knapp 13

What does docking mean?

trying to find the „best matching“ between 2 molecules

23.02.2012 Bernhard Knapp 14

23.02.2012 Bernhard Knapp 16

23.02.2012 Bernhard Knapp 17

Why is docking useful?

 Docking (~Virtual Screening) is of paramount interest for drug discovery

23.02.2012 Bernhard Knapp 18

1) Decide how to search through the spatial space

2) Decide how flexible ligand and receptor can be

3) Decide how to score various parameter sets

23.02.2012 Bernhard Knapp 19

Where is the difficulty?

1) 6 degrees of freedom in 3d space (3 translational, 3 rotational)

23.02.2012 Bernhard Knapp 21

Ad 2) Deciding about the flexibility

 “induced fit” docking

23.02.2012 Bernhard Knapp 22

 Force Field based scoring function

23.02.2012 Bernhard Knapp 23

Scoring Funktionen (2/2)

 Knowledge based scoring function

23.02.2012 Bernhard Knapp 24

"relatively small chemical modifications can lead to significant changes in

[Kitchen et al., 2004]

23.02.2012 Bernhard Knapp [Sousa, 2006] 26

Correct result vs incorrect result

23.02.2012 Bernhard Knapp 29

23.02.2012 Bernhard Knapp 30

 “AutoDock is a suite of automated docking tools. It is designed to predict

23.02.2012 Bernhard Knapp 31

search algorithms used for spatial space

23.02.2012 Bernhard Knapp 32

 “induced fit” docking

23.02.2012 Bernhard Knapp 33

Scoring functions (1/2)

 Force Field based scoring function

23.02.2012 Bernhard Knapp 34

Build up proteins (german “Eiweiß”)

20 different canonical amino acids (AAs) are existing (that means 20

Primary structure: the pure sequence of the AAs

Secondary structure: e.g. beta-sheet, alpha-helix, or turns

Tertiary structure: 3D arrangement of secondary structure

Quaternary structure: several proteins together

Ligand: also known as (small) peptide, epitope, guest, antigenic

Docking (~Virtual Screening) is of paramount interest for drug discovery

“induced fit” docking

Force Field based scoring function

Knowledge based scoring function

“AutoDock is a suite of automated docking tools. It is designed to predict

“induced fit” docking

Force Field based scoring function

Knowledge based scoring function

Idea: local neighborhood search but „sometimes“ accepting worse

receptor hold rigid

the weighting factors W have been calibrated on a set of 188

75 cases: found but other

Computational methods can be used to identify potential drugs

MD is a type of computer simulation

Newton’s equations of motion describe classical mechanics, not

First idea: difference of the single frames (transparent) from starting

A similar measurement is the radius of gyration. It measures the