SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information.

Marco Biasini,Konstantin Arnold,Torsten Schwede,Florian Kiefer,Stefan Bienert,Lorenza Bordoli,Tiziano Gallo Cassarino,Martino Bertoni,Tobias Schmidt,Gabriel Studer,Andrew Waterhouse

doi:10.1093/nar/gku340

Marco Biasini, Konstantin Arnold + Show 9 more

Open Access

https://doi.org/10.1093/nar/gku340

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Abstract

Protein structure homology modelling has become a routine technique to generate 3D models for proteins when experimental structures are not available. Fully automated servers such as SWISS-MODEL with user-friendly web interfaces generate reliable models without the need for complex software packages or downloading large databases. Here, we describe the latest version of the SWISS-MODEL expert system for protein structure modelling. The SWISS-MODEL template library provides annotation of quaternary structure and essential ligands and co-factors to allow for building of complete structural models, including their oligomeric structure. The improved SWISS-MODEL pipeline makes extensive use of model quality estimation for selection of the most suitable templates and provides estimates of the expected accuracy of the resulting models. The accuracy of the models generated by SWISS-MODEL is continuously evaluated by the CAMEO system. The new web site allows users to interactively search for templates, cluster them by sequence similarity, structurally compare alternative templates and select the ones to be used for model building. In cases where multiple alternative template structures are available for a protein of interest, a user-guided template selection step allows building models in different functional states. SWISS-MODEL is available at http://swissmodel.expasy.org/.

Highlights

SWISS-MODEL is an automated system for modelling the 3D structure of a protein from its amino acid sequence using homology modelling techniques
A newly developed interactive web interface allows users to conveniently search for suitable templates using sensitive Hidden Markov Models (HMM) searches against the SWISS-MODEL Template Library (SMTL), analyse alternative templates and alignments, perform structural superposition and comparison, explore ligands and cofactors in templates and compare the resulting models using mean force potential based model quality estimation tools
With the new version of SWISS-MODEL presented here, we aimed to address these aspects by introducing a new augmented SWISS-MODEL Template Library, which includes information on quaternary structures and the role of ligands bound to the template

Summary

Introduction

SWISS-MODEL (http://swissmodel.expasy.org/) is an automated system for modelling the 3D structure of a protein from its amino acid sequence using homology modelling techniques. SWISS-MODEL has been established 20 years ago as the first fully automated server for protein structure homology modelling and has been continuously developed and improved since [1,2,3,4]. A newly developed interactive web interface allows users to conveniently search for suitable templates using sensitive Hidden Markov Models (HMM) searches against the SWISS-MODEL Template Library (SMTL), analyse alternative templates and alignments, perform structural superposition and comparison, explore ligands and cofactors in templates and compare the resulting models using mean force potential based model quality estimation tools

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