Protein structure homology modeling using SWISS-MODEL workspace

• Published in: Nature protocols Vol. 4; no. 1; pp. 1 - 13
• Main Authors: Schwede, Torsten, Bordoli, Lorenza, Kiefer, Florian, Arnold, Konstantin, Benkert, Pascal, Battey, James
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 01.01.2009; Nature Publishing Group
• Subjects: Amino Acid Sequence; Analysis; Analytical Chemistry; Bioinformatics; Biological Techniques; Biomedical and Life Sciences; Computational biology; Computational Biology - methods; Computational Biology/Bioinformatics; Databases, Genetic; Expert systems; Internet; Life Sciences; Microarrays; Models, Molecular; Organic Chemistry; Protein Conformation; Protein-protein interactions; Proteins; Proteins - chemistry; protocol; Sequence Homology; Software; Structural models; Structure; Switzerland
• ISSN: 1754-2189; 1750-2799
• DOI: 10.1038/nprot.2008.197

Homology modeling aims to build three-dimensional protein structure models using experimentally determined structures of related family members as templates. SWISS-MODEL workspace is an integrated Web-based modeling expert system. For a given target protein, a library of experimental protein structures is searched to identify suitable templates. On the basis of a sequence alignment between the target protein and the template structure, a three-dimensional model for the target protein is generated. Model quality assessment tools are used to estimate the reliability of the resulting models. Homology modeling is currently the most accurate computational method to generate reliable structural models and is routinely used in many biological applications. Typically, the computational effort for a modeling project is less than 2 h. However, this does not include the time required for visualization and interpretation of the model, which may vary depending on personal experience working with protein structures.