FUNCTIONAL GENOMICS

MODULE-I
FUNCTIONAL GENOMICS
M.SC. MICROBIOLOGY/BIOTECHNOLOGY 2022-24

ABHILASH JEAS GEORGE

M.SC. MICROBIOLOGY

1
 Introduction
• SWISS-MODEL is a fully automated protein structure
homology-modelling server, accessible via the Expasy web
server, or from the program DeepView (Swiss Pdb-Viewer).
• The purpose of this server is to make protein modelling
accessible to all life science researchers worldwide.
• SWISS-MODEL is developed by the Computational
Structural Biology Group at the SIB Swiss Institute of
Bioinformatics and the Biozentrum of the University of
Basel.
2
SWISS-MODEL Homepage

Link: https://swissmodel.expasy.org/ 3
 Basics of modelling
• Building a homology model comprises four main steps:
i. identification of structural template(s)
ii. alignment of target sequence and template structure(s)
iii. model-building, and
iv. model quality evaluation.
• These steps require specialised software and integrate up-to-date
protein sequence and structure databases.
• Each of the above steps can be repeated interactively until a satisfying
modelling result is achieved.
4
 The SWISS-MODEL Workspace
• The SWISS-MODEL Workspace is a personal web-based working
environment, where several modelling projects can be carried out in
parallel.
• Tools for template selection, model building, and structure quality
evaluation can be invoked from within the workspace directly or via the
web page menu.
• From the workspace, the user accesses the current modelling projects,
inspects their status and visualizes the results upon job completion.
• Project names can be changed retroactively by clicking on the symbol next
to the project title.
• By default, projects are stored for two weeks on the server with an option
to extend the project lifetime. The remaining time until a given project is
deleted from the server is displayed accordingly.
5
 Modelling methods
Depending on the difficulty of the modelling task, three different types of
modelling modes are provided: automated mode, alignment mode, and project
mode.
• Automated Mode: The Automated Mode only requires the amino acid sequence
or the UniProtKB accession code of the target protein as input. The automatic
pipeline identifies suitable templates based on BLAST and HHblits. The resulting
templates are ranked according to the expected quality of the resulting models.
• Alignment Mode: If the desired template for modelling is known and available in
the SWISS-MODEL Template Library (SMTL), a target–template alignment in
either FASTA or Clustal format may be used to start the modelling process,
thereby skipping the template search.
• Project Mode: In difficult modelling situations, where the correct alignment
between target and template cannot be clearly determined by sequence-based
methods, visual inspection and manual manipulation of the alignment can help
improving the quality of the resulting model significantly.
6
 SWISS-MODEL modelling workflow
Input data: The target protein can be provided as amino acid sequence, either in FASTA, Clustal
format or as a plain text. Alternatively, a UniProtKB accession code can be specified.

Template search: Data provided in step 1 serve as a query to search for evolutionary related protein
structures against the SWISS-MODEL template library (SMTL) using BLAST and HHBits.

Template selection: When the template search is complete, templates are ranked according to
expected quality of the resulting models, as estimated by Global Model Quality Estimate (GMQE)
and Quaternary Structure Quality Estimate (QSQE).
Top-ranked templates and alignments are compared to verify whether they represent alternative
conformational states or cover different regions of the target protein

7
Model building: For each selected template, a 3D protein model is automatically
generated by first transferring conserved atom coordinates as defined by the
target-template alignment. SWISS-MODEL relies on the OpenStructure
computational structural biology framework and the ProMod3 modelling engine to
perform this step.

Model quality estimation: To quantify modelling errors and give estimates on

expected model accuracy, SWISS-MODEL relies on the QMEAN scoring function.

8
 Model evaluation
Global model evaluation
• GMQE and QMEANDisCo global give an overall model quality
measurement between 0 and 1, with higher numbers indicating
higher expected quality.
• GMQE is coverage dependent, i.e., a model covering only half of the
target sequence is unlikely to get a score above 0.5.
• QMEANDisCo on the other hand evaluates the model 'as is' without
explicit coverage dependency.

9
 How to do the modelling?

Click the "Start Modelling" button or select the option "myWorkspace" from the
navigation bar (Modelling → myWorkspace) to start a new modelling project.
10
 SEQUENCE OR UNIPROTKB AC TO BE
TYPED/PASTED HERE

• You can either paste the protein sequence or provide the UniprotKB AC of your
target sequence in the input form.
• A project title is automatically suggested from the information retrieved from
SWISS-MODEL's own copy of the UniprotKB annotation, if a UniProtKB AC is used.
11
• To search for available template structures, click on the “Search for
Templates” button OR you can directly build model also.
• NOTE: Minimum amino acids count should be 30.
12
• Once the search is started, you can verify the status of the job, and
optionally you can bookmark the page using the provided link and
come later to visualise the results. Otherwise you need to wait until
the search finishes.
• Note: By using the "Build Model" option, an automatic pipeline will
run both the template search and the template selection steps.
• The automated mode selects templates that maximise the expected
quality of the model. However, this does not guarantee that the best
template available is selected.
• Depending on the intended application of a model, selecting a
different template than the top-ranked one might be necessary.

13
• When the template search is finished, the output page includes a
main table showing the list of available templates ranked according
to the expected quality of the resulting models.
• For each template, the following information is provided:
• A checkbox to select and visualise the template in the 3D panel
• The SMTL ID of the template and a link to the SWISS-MODEL
Template Library page associated to that SMTL entry
• The protein name of the template
• The coverage to the target sequence
• The GMQE (Global Model Quality Estimation)
• The QSQE (Quaternary Structure Quality Estimation)
• The target–template sequence identity
14
By clicking on the checkbox, different template structures can be visualized and compared to
by structure superposition in the 3D viewer. 15
• More details available are:
• The experimental method used to determine the structure (and
resolution, if applicable)
• The oligomeric state of the SMTL biounit
• The ligands present in the experimental structure (if any)
• A clickable icon to expand the box with the description of the
template
As you can see in the next slide, there are multiple templates which
cover the complete sequence and share a considerable sequence
identity with our target sequence.

16
17
To get an overview of the similarity between the selected templates click on the
"Sequence Similarity" tab. 18
By looking at the "Alignment" tab, you can notice that the sequences
of the selected templates are very similar overall.
19
After you
have selected
the
template(s),
click the
'Build Model'
button to run
the modelling
job.

20
• For each model generated based on the selected templates, the following
information is provided:
• A file containing the model coordinates along with relevant information
on the modelling process
• The oligomeric state of the model
• The modelled ligands
• QMEAN model quality estimation results
• The target–template sequence alignment
• The template name (SMTL ID)
• The sequence identity to the target
• The target sequence coverage
• Models can be displayed interactively using the 3D viewer. By default,
models are colored by model quality estimates assigned by QMEAN to
highlight regions of the model which are well- or poorly modelled.
21
22
Download your
modelled protein in
any format

23
 Applications of SWISS-MODEL (≈Homology
modelling)
• Prediction of protein structures that are difficult to obtain
experimentally using techniques like X-ray crystallography or NMR.
• Predict the functional properties of proteins with unknown
structures by modeling the protein structure and comparing it with
known structures of related proteins.
• Useful in studying the evolution of protein families by comparing the
structures of related proteins from different species to identify the
changes that have occurred during evolution.
• Used to identify potential drug targets by predicting the structure of
a protein to understand its function and identify potential sites for
drug binding (docking studies).
24
 References
• https://swissmodel.expasy.org/docs/help
• https://swissmodel.expasy.org/docs/examples
• Waterhouse A, Bertoni M, Bienert S, et al. SWISS-MODEL: homology
modelling of protein structures and complexes. Nucleic Acids Res.
2018;46(W1):W296-W303. doi:10.1093/nar/gky427

25