Swiss-model

SWISS-MODEL is a structural bioinformatics web-server

dedicated to homology modeling of 3D protein
SWISS-MODEL
structures.[1][2] Homology modeling is currently the most Type Structural bioinformatics tool
accurate method to generate reliable three-dimensional protein License free for use, source code not
structure models and is routinely used in many practical
available
applications. Homology (or comparative) modelling methods
make use of experimental protein structures ("templates") to Website https://swissmodel.expasy.org/
build models for evolutionary related proteins ("targets").

Today, SWISS-MODEL consists of three tightly integrated components: (1) The SWISS-MODEL pipeline
– a suite of software tools and databases for automated protein structure modelling,[1] (2) The SWISS-
MODEL Workspace – a web-based graphical user workbench,[2] (3) The SWISS-MODEL Repository – a
continuously updated database of homology models for a set of model organism proteomes of high
biomedical interest.[3]

Pipeline
SWISS-MODEL pipeline comprises the four main steps that are involved in building a homology model of
a given protein structure:

1. Identification of structural template(s). BLAST and HHblits are used to identify templates.
The templates are stored in the SWISS-MODEL Template Library (SMTL), which is derived
from PDB.
2. Alignment of target sequence and template structure(s).
3. Model building and energy minimization. SWISS-MODEL implements a rigid fragment
assembly approach for modelling.
4. Assessment of the model's quality using QMEAN, a statistical potential of mean force.

Workspace
The SWISS-MODEL Workspace integrates programs and databases required for protein structure
modelling in a web-based workspace. Depending on the complexity of the modelling task, different modes
of usage can be applied, in which the user has different levels of control over individual modelling steps:
automated mode, alignment mode, and project mode. A fully automated mode is used when a sufficiently
high sequence identity between target and template (>50%) allows for no human intervention at all. In this
case only the sequence or UniProt accession code of the protein is required as input. The alignment mode
enables the user to input their own target-template alignments from which the modelling procedure starts
(i.e. search for templates step is skipped and rarely only minor changes in the provided alignment are
made). The project mode is used in more difficult cases, when manual corrections of target-template
alignments are needed to improve the quality of the resulting model. In this mode the input is a project file
that can be generated by the DeepView (Swiss Pdb Viewer) visualization and structural analysis tool,[4] to
allow the user to examine and manipulate the target-template alignment in its structural context. In all three
cases the output is a pdb file with atom coordinates of the model or a DeepView project file. The four main
steps of homology modelling may be repeated iteratively until a satisfactory model is achieved.
The SWISS-MODEL Workspace is accessible via the ExPASy web server, or it can be used as part of the
program DeepView (Swiss Pdb-Viewer). As of September 2015 it has been cited 20000 times in scientific
literature,[5] making it one of the most widely used tools for protein structure modelling. The tool is free for
academic use.

Repository
The SWISS-MODEL Repository provides access to an up-to-date collection of annotated three-
dimensional protein models for a set of model organisms of high general interest. Model organisms include
human,[6] mouse,[7] C.elegans,[8] E.coli,[9] and various pathogens including severe acute respiratory
syndrome coronavirus 2 (SARS-CoV-2).[10] SWISS-MODEL Repository is integrated with several
external resources, such as UniProt,[11] InterPro,[12] STRING,[13] and Nature PSI SBKB.[14]

New developments of the SWISS-MODEL expert system feature (1) automated modelling of homo-
oligomeric assemblies; (2) modelling of essential metal ions and biologically relevant ligands in protein
structures; (3) local (per-residue) model reliability estimates based on the QMEAN local score function;[15]
(4) mapping of UniProt features to models. (1) and (2) are available when using the automated mode of the
SWISS-MODEL Workspace; (3) is always provided when calculating an homology model using the
SWISS-MODEL Workspace, and (4) is available in the SWISS-MODEL Repository.

Accuracy and reliability of the method

In the past, the accuracy, stability and reliability of the SWISS-MODEL server pipeline was validated by
the EVA-CM benchmark project. Currently, the SWISS-MODEL server pipeline is participating in the
CAMEO3D [1] (https://www.cameo3d.org) (Continuous Automated Model EvaluatiOn) project which
continuously evaluates the accuracy and reliability of protein structure prediction services in a fully
automated manner.

References
1. Schwede T, Kopp J, Guex N, Peitsch MC (2003). "SWISS-MODEL: an automated protein
homology-modeling server" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC168927).
Nucleic Acids Research. 31 (13): 3381–3385. doi:10.1093/nar/gkg520 (https://doi.org/10.109
3%2Fnar%2Fgkg520). PMC 168927 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC16892
7). PMID 12824332 (https://pubmed.ncbi.nlm.nih.gov/12824332).
2. Biasini M, Bienert S, Waterhouse A, Arnold K, Studer G, Schmidt T, Kiefer F, Cassarino TG,
Bertoni M, Bordoli L, Schwede T (2014). "SWISS-MODEL: modelling protein tertiary and
quaternary structure using evolutionary information" (https://www.ncbi.nlm.nih.gov/pmc/articl
es/PMC4086089). Nucleic Acids Research. 42 (W1): 195–201. doi:10.1093/nar/gku340 (http
s://doi.org/10.1093%2Fnar%2Fgku340). PMC 4086089 (https://www.ncbi.nlm.nih.gov/pmc/ar
ticles/PMC4086089). PMID 24782522 (https://pubmed.ncbi.nlm.nih.gov/24782522).
3. Bienert S, Waterhouse A, de Beer TA, Tauriello G, Studer G, Bordoli L, Schwede T (2017).
"The SWISS-MODEL Repository-new features and functionality" (https://www.ncbi.nlm.nih.g
ov/pmc/articles/PMC5210589). Nucleic Acids Research. 45 (D1): D313–D319.
doi:10.1093/nar/gkw1132 (https://doi.org/10.1093%2Fnar%2Fgkw1132). PMC 5210589 (http
s://www.ncbi.nlm.nih.gov/pmc/articles/PMC5210589). PMID 27899672 (https://pubmed.ncbi.
nlm.nih.gov/27899672).
 4. Guex N, Peitsch MC, Schwede T (2009). "Automated comparative protein structure
modeling with SWISS-MODEL and Swiss-PdbViewer: a historical perspective".
Electrophoresis. 30 (Suppl 1): S162–173. doi:10.1002/elps.200900140 (https://doi.org/10.10
02%2Felps.200900140). PMID 19517507 (https://pubmed.ncbi.nlm.nih.gov/19517507).
S2CID 39507113 (https://api.semanticscholar.org/CorpusID:39507113).
5. Number of results returned from a search in Google Scholar. (Google Scholar) (https://schola
r.google.de/scholar?hl=en&q=%22swiss-model%22+%2Bprotein&btnG=Search&as_allsubj
=some&as_subj=bio&as_subj=chm&as_subj=eng&as_subj=med&as_sdt=1%2C5&as_ylo=
&as_vis=0)
6. "SWISS-MODEL | Homo sapiens" (https://swissmodel.expasy.org/repository/species/9606).
swissmodel.expasy.org. Retrieved 2020-02-14.
7. "SWISS-MODEL | Mus musculus" (https://swissmodel.expasy.org/repository/species/10090).
swissmodel.expasy.org. Retrieved 2020-02-14.
8. "SWISS-MODEL | Caenorhabditis elegans" (https://swissmodel.expasy.org/repository/speci
es/6239). swissmodel.expasy.org. Retrieved 2020-02-14.
9. "SWISS-MODEL | Escherichia coli" (https://swissmodel.expasy.org/repository/species/8333
3). swissmodel.expasy.org. Retrieved 2020-02-14.
10. "SWISS-MODEL | SARS-CoV-2" (https://swissmodel.expasy.org/repository/species/269704
9). swissmodel.expasy.org. Retrieved 2020-02-14.
11. Wu CH, Apweiler R, Bairoch A, et al. (2006). "The Universal Protein Resource (UniProt): an
expanding universe of protein information" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1
347523). Nucleic Acids Research. 34 (Database issue): D187–91. doi:10.1093/nar/gkj161 (h
ttps://doi.org/10.1093%2Fnar%2Fgkj161). PMC 1347523 (https://www.ncbi.nlm.nih.gov/pmc/
articles/PMC1347523). PMID 16381842 (https://pubmed.ncbi.nlm.nih.gov/16381842).
12. Wu CH, Apweiler R, Bairoch A, et al. (2007). InterPro and InterProScan: tools for protein
sequence classification and comparison. Methods in Molecular Biology. Vol. 396. pp. 59–70.
doi:10.1007/978-1-59745-515-2_5 (https://doi.org/10.1007%2F978-1-59745-515-2_5).
ISBN 978-1-934115-37-4. PMID 18025686 (https://pubmed.ncbi.nlm.nih.gov/18025686).
13. Szklarczyk D, Franceschini A, Kuhn M, et al. (2011). "The STRING database in 2011:
functional interaction networks of proteins, globally integrated and scored" (https://www.ncbi.
nlm.nih.gov/pmc/articles/PMC3013807). Nucleic Acids Research. 39 (Database issue):
D561–8. doi:10.1093/nar/gkq973 (https://doi.org/10.1093%2Fnar%2Fgkq973).
PMC 3013807 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013807). PMID 21045058
(https://pubmed.ncbi.nlm.nih.gov/21045058).
14. Gabanyi MJ, Adams PD, Arnold K, et al. (2011). "The Structural Biology Knowledgebase: a
portal to protein structures, sequences, functions, and methods" (https://www.ncbi.nlm.nih.go
v/pmc/articles/PMC3123456). Journal of Structural and Functional Genomics. 12 (2): 45–54.
doi:10.1007/s10969-011-9106-2 (https://doi.org/10.1007%2Fs10969-011-9106-2).
PMC 3123456 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3123456). PMID 21472436
(https://pubmed.ncbi.nlm.nih.gov/21472436).
15. Benkert P, Kunzli M, Schwede T (2009). "QMEAN server for protein model quality
estimation" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2703985). Nucleic Acids
Research. 37 (Web Server issue): W510–4. doi:10.1093/nar/gkp322 (https://doi.org/10.109
3%2Fnar%2Fgkp322). PMC 2703985 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC27039
85). PMID 19429685 (https://pubmed.ncbi.nlm.nih.gov/19429685).

External links
SWISS-MODEL (https://swissmodel.expasy.org/)
See also
Homology modelling
Protein structure prediction
Protein structure prediction software
CASP (Critical Assessment of Techniques for Protein Structure Prediction)

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