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SWISS-MODEL: homology modelling of protein structures and complexes

Nucleic Acids Research · 2018 · Vol. 46(W1) · pp. W296–W303

Andrew Waterhouse(SIB Swiss Institute of Bioinformatics)Martino Bertoni(SIB Swiss Institute of Bioinformatics)Stefan Bienert(SIB Swiss Institute of Bioinformatics)Gabriel Studer(SIB Swiss Institute of Bioinformatics)Gerardo Tauriello(SIB Swiss Institute of Bioinformatics)Rafal Gumienny(SIB Swiss Institute of Bioinformatics)Florian Heer(SIB Swiss Institute of Bioinformatics)Tjaart de Beer(SIB Swiss Institute of Bioinformatics)Christine Rempfer(SIB Swiss Institute of Bioinformatics)Lorenza Bordoli(SIB Swiss Institute of Bioinformatics)Rosalba Lepore(SIB Swiss Institute of Bioinformatics)Torsten Schwede✉(SIB Swiss Institute of Bioinformatics)

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Abstract

Homology modelling has matured into an important technique in structural biology, significantly contributing to narrowing the gap between known protein sequences and experimentally determined structures. Fully automated workflows and servers simplify and streamline the homology modelling process, also allowing users without a specific computational expertise to generate reliable protein models and have easy access to modelling results, their visualization and interpretation. Here, we present an update to the SWISS-MODEL server, which pioneered the field of automated modelling 25 years ago and been continuously further developed. Recently, its functionality has been extended to the modelling of homo- and heteromeric complexes. Starting from the amino acid sequences of the interacting proteins, both the stoichiometry and the overall structure of the complex are inferred by homology modelling. Other major improvements include the implementation of a new modelling engine, ProMod3 and the introduction a new local model quality estimation method, QMEANDisCo. SWISS-MODEL is freely available at https://swissmodel.expasy.org.

Protein Structure and Dynamics Microbial Metabolic Engineering and Bioproduction Bioinformatics and Genomic NetworksHomology modelingWorkflowBiologyHomology (biology)Computational biologyVisualizationComputer scienceBioinformaticsData miningAmino acid

MeSH terms

Models, ChemicalProtein ConformationProteinsSoftwareSequence Homology, Amino AcidInternetDatabases, ProteinStructural Homology, ProteinMolecular Dynamics Simulation