The SWISS-MODEL Workspace: A Web-Based Environment for Protein Structure Homology Modelling

Bioinformatics. 2006 Jan 15;22(2):195-201. doi: 10.1093/bioinformatics/bti770. Epub 2005 Nov 13.

Abstract

Motivation: Homology models of proteins are of great interest for planning and analysing biological experiments when no experimental three-dimensional structures are available. Building homology models requires specialized programs and up-to-date sequence and structural databases. Integrating all required tools, programs and databases into a single web-based workspace facilitates access to homology modelling from a computer with web connection without the need of downloading and installing large program packages and databases.

Results: SWISS-MODEL workspace is a web-based integrated service dedicated to protein structure homology modelling. It assists and guides the user in building protein homology models at different levels of complexity. A personal working environment is provided for each user where several modelling projects can be carried out in parallel. Protein sequence and structure databases necessary for modelling are accessible from the workspace and are updated in regular intervals. Tools for template selection, model building and structure quality evaluation can be invoked from within the workspace. Workflow and usage of the workspace are illustrated by modelling human Cyclin A1 and human Transmembrane Protease 3.

Availability: The SWISS-MODEL workspace can be accessed freely at http://swissmodel.expasy.org/workspace/

Publication types

  • Evaluation Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Amino Acid Sequence
  • Computer Simulation
  • Databases, Protein
  • Internet*
  • Models, Chemical
  • Models, Molecular*
  • Molecular Sequence Data
  • Online Systems
  • Protein Conformation
  • Proteins / analysis
  • Proteins / chemistry*
  • Proteins / classification
  • Sequence Alignment / methods*
  • Sequence Analysis, Protein / methods*
  • Sequence Homology, Amino Acid
  • Software*
  • Systems Integration
  • User-Computer Interface*

Substances

  • Proteins