SWISS-MODEL: an automated protein homology-modeling server

• Published in: Nucleic acids research 2003-07, Vol.31 (13), p.3381-3385
• Main Authors: Schwede, Torsten, Kopp, Jürgen, Guex, Nicolas, Peitsch, Manuel C.
• Format: Article
• Language: English
• Subjects: Computer Graphics; Internet; Models, Molecular; Proteins - chemistry; Sequence Alignment; Sequence Analysis, Protein; Software; Structural Homology, Protein; User-Computer Interface
• ISSN: 0305-1048; 1362-4962; 1362-4962
• DOI: 10.1093/nar/gkg520

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.