Nucleic Acids Research, 2003, Vol. 31, No. 13 3381-3385
© 2003 Oxford University Press
SWISS-MODEL: an automated protein homology-modeling server
1 Biozentrum der Universität Basel, Klingelbergstr. 50-70, CH 4056 Basel, Switzerland 2 Swiss Institute of Bioinformatics, Basel, Switzerland 3 GlaxoSmithKline, Research Triangle Park, NC 27709, USA 4 Novartis AG, 4002 Basel, Switzerland
*To whom correspondence should be addressed. Tel: +41 612671581; Fax: +41 612671584; Email: torsten.schwede{at}unibas.ch
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.
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