SWISS-MODEL: An automated protein homology-modeling server - PubMed (original) (raw)

SWISS-MODEL: An automated protein homology-modeling server

Torsten Schwede et al. Nucleic Acids Res. 2003.

Abstract

SWISS-MODEL (http://swissmodel.expasy.org) is a server for automated comparative modeling of three-dimensional (3D) protein structures. It pioneered the field of automated modeling starting in 1993 and is the most widely-used free web-based automated modeling facility today. In 2002 the server computed 120 000 user requests for 3D protein models. SWISS-MODEL provides several levels of user interaction through its World Wide Web interface: in the 'first approach mode' only an amino acid sequence of a protein is submitted to build a 3D model. Template selection, alignment and model building are done completely automated by the server. In the 'alignment mode', the modeling process is based on a user-defined target-template alignment. Complex modeling tasks can be handled with the 'project mode' using DeepView (Swiss-PdbViewer), an integrated sequence-to-structure workbench. All models are sent back via email with a detailed modeling report. WhatCheck analyses and ANOLEA evaluations are provided optionally. The reliability of SWISS-MODEL is continuously evaluated in the EVA-CM project. The SWISS-MODEL server is under constant development to improve the successful implementation of expert knowledge into an easy-to-use server.

PubMed Disclaimer

Figures

Figure 1

Figure 1

SWISS-MODEL project displayed in DeepView. Project files contain the final model coordinates, accompanied by the superposed template structures. Adjustments of the underlying target-template alignment can be done manually. DeepView provides several tools to visualize and analyze the modeling results.

Similar articles

Cited by

References

    1. Westbrook J., Feng,Z., Chen,L., Yang,H. and Berman,H.M. (2003) The Protein Data Bank and structural genomics. Nucleic Acids Res., 31, 489–491. - PMC - PubMed
    1. Boeckmann B., Bairoch,A., Apweiler,R., Blatter,M.-C., Estreicher,A., Gasteiger,E., Martin,M.J., Michoud,K., O'Donovan,C., Phan,I. et al. (2003) The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res., 31, 365–370. - PMC - PubMed
    1. Tramontano A., Leplae,R. and Morea,V. (2001) Analysis and assessment of comparative modeling predictions in CASP4. Proteins, 45 (Suppl. 5), 22–38. - PubMed
    1. Marti-Renom M.A., Stuart,A.C., Fiser,A., Sanchez,R., Melo,F. and Sali,A. (2000) Comparative protein structure modeling of genes and genomes. Annu. Rev. Biophys. Biomol. Struct., 29, 291–325. - PubMed
    1. Brenner S.E. (2001) A tour of structural genomics. Nature Rev. Genet., 2, 801–809. - PubMed

Publication types

MeSH terms

Substances

LinkOut - more resources