SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information.
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/.
Biozentrum, University of Basel, Basel 4056, Switzerland SIB Swiss Institute of Bioinformatics, Basel 4056, Switzerland.
Marco
M
Biasini
Biozentrum, University of Basel, Basel 4056, Switzerland SIB Swiss Institute of Bioinformatics, Basel 4056, Switzerland.
Stefan
S
Bienert
Biozentrum, University of Basel, Basel 4056, Switzerland SIB Swiss Institute of Bioinformatics, Basel 4056, Switzerland.
Andrew
A
Waterhouse
Biozentrum, University of Basel, Basel 4056, Switzerland SIB Swiss Institute of Bioinformatics, Basel 4056, Switzerland.
Konstantin
K
Arnold
Biozentrum, University of Basel, Basel 4056, Switzerland SIB Swiss Institute of Bioinformatics, Basel 4056, Switzerland.
Gabriel
G
Studer
Biozentrum, University of Basel, Basel 4056, Switzerland SIB Swiss Institute of Bioinformatics, Basel 4056, Switzerland.
Tobias
T
Schmidt
Biozentrum, University of Basel, Basel 4056, Switzerland SIB Swiss Institute of Bioinformatics, Basel 4056, Switzerland.
Florian
F
Kiefer
Biozentrum, University of Basel, Basel 4056, Switzerland SIB Swiss Institute of Bioinformatics, Basel 4056, Switzerland.
Tiziano
T
Gallo Cassarino
Biozentrum, University of Basel, Basel 4056, Switzerland SIB Swiss Institute of Bioinformatics, Basel 4056, Switzerland.
Martino
M
Bertoni
Biozentrum, University of Basel, Basel 4056, Switzerland SIB Swiss Institute of Bioinformatics, Basel 4056, Switzerland.
Lorenza
L
Bordoli
Biozentrum, University of Basel, Basel 4056, Switzerland SIB Swiss Institute of Bioinformatics, Basel 4056, Switzerland Torsten.schwede@unibas.ch.
Torsten
T
Schwede
D019143:Evolution, Molecular; D020407:Internet; D008958:Models, Molecular; D020836:Protein Structure, Quaternary; D017434:Protein Structure, Tertiary; D012984:Software; D040681:Structural Homology, Protein