Protein structure homology modeling using SWISS-MODEL workspace.

Nature Protocols
Lorenza BordoliTorsten Schwede

Abstract

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.

References

Dec 5, 1993·Journal of Molecular Biology·A Sali, T L Blundell
Oct 1, 1995·Trends in Biochemical Sciences·E SeebergM Bjørås
May 23, 1996·Nature·R W HooftE E Abola
Jun 1, 1996·Current Opinion in Structural Biology·M Vingron
Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
May 22, 1998·Journal of Molecular Biology·F Melo, E Feytmans
Jun 26, 1998·The Biochemical Journal·H Mellor, P J Parker
Oct 27, 1998·Trends in Biochemical Sciences·K Henrick, J M Thornton
Apr 9, 1999·Protein Engineering·B Rost
Jun 11, 1999·Current Opinion in Structural Biology·M R Groves, D Barford
Jun 24, 2000·Research in Microbiology·T SchwedeM C Peitsch
Aug 15, 2000·Annual Review of Biophysics and Biomolecular Structure·M A Martí-RenomA Sali
Oct 25, 2000·Protein Science : a Publication of the Protein Society·A FiserA Sali
Oct 6, 2001·Science·D Baker, A Sali
Jul 16, 2002·Bioinformatics·Manuel C Peitsch
Jun 26, 2003·Nucleic Acids Research·Ingrid Y Y KohBurkhard Rost
Jun 26, 2003·Nucleic Acids Research·Narayanan EswarAndrej Sali
Jun 26, 2003·Nucleic Acids Research·Torsten SchwedeManuel C Peitsch
Jul 10, 2003·Chemical Reviews·James T Stivers, Yu Lin Jiang
Jul 10, 2003·Journal of Molecular Biology·Michael L TressAlfonso Valencia
Aug 22, 2003·Protein Science : a Publication of the Protein Society·Adrian A CanutescuRoland L Dunbrack
Oct 28, 2003·Proteins·Anna Tramontano, Veronica Morea
Dec 19, 2003·Nucleic Acids Research·Alex BatemanSean R Eddy
Dec 19, 2003·Nucleic Acids Research·Antonina AndreevaAlexey G Murzin
Dec 19, 2003·Nucleic Acids Research·Jürgen Kopp, Torsten Schwede
May 29, 2004·Pharmacogenomics·Jurgen Kopp, Torsten Schwede
Jul 29, 2004·Drug Discovery Today·Alexander HillischRolf Hilgenfeld
Nov 9, 2004·Bioinformatics·Johannes Söding
Nov 20, 2004·Nucleic Acids Research·Jesper J SørensenMichael Petersen
Dec 21, 2004·Nucleic Acids Research·David L WheelerEugene Yaschenko
Feb 19, 2005·Current Opinion in Structural Biology·Patrick AloyRobert B Russell
Feb 19, 2005·Current Opinion in Structural Biology·Anthony L Fink
Mar 2, 2005·Nature Reviews. Molecular Cell Biology·H Jane Dyson, Peter E Wright
Jun 28, 2005·Nucleic Acids Research·Johannes SödingAndrei N Lupas
Sep 10, 2005·Bioinformatics·Xiang ZhangAhmed K Elmagarmid
Sep 28, 2005·Proteins·Michael TressAlfonso Valencia
Nov 23, 2005·Bioinformatics·Konstantin ArnoldTorsten Schwede

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Citations

Feb 19, 2013·Biochimica Et Biophysica Acta·Ran FriedmanKjersti Flatmark
Mar 5, 2013·Veterinary Immunology and Immunopathology·Xinxin ZhaoXun Suo
Jul 14, 2012·Genetics in Medicine : Official Journal of the American College of Medical Genetics·Wayne I L DaviesAndrea H Németh
Aug 28, 2013·Nature Communications·Cindy J CastelleJillian F Banfield
Mar 5, 2013·Nature Neuroscience·Joshua LevitzEhud Y Isacoff
Mar 22, 2012·Proceedings of the National Academy of Sciences of the United States of America·Elena Fernandez-FueyoDan Cullen
Jul 23, 2013·Proceedings of the National Academy of Sciences of the United States of America·Ivan GushchinValentin Gordeliy
Nov 13, 2013·Proceedings of the National Academy of Sciences of the United States of America·Vijaykumar KaruppiahJeremy P Derrick
Jun 18, 2009·The Journal of Biological Chemistry·Katy L EverettMatilda Katan
Feb 10, 2012·The Journal of Biological Chemistry·María de la FuenteMarvin T Nieman
Mar 23, 2012·The Journal of Biological Chemistry·Elena Fernández-FueyoAngel T Martínez
Apr 26, 2013·The Journal of Biological Chemistry·Sophie Réhault-GodbertYves Nys
Mar 15, 2012·Molecular & Cellular Proteomics : MCP·Jiang-Ming SunWen-Wei Xiong
Aug 28, 2013·The Journal of General Physiology·Matthew D PerryJamie I Vandenberg
Aug 25, 2010·Bioinformatics·Marco BiasiniAnsgar Philippsen
Dec 8, 2010·Bioinformatics·Pascal BenkertTorsten Schwede
Apr 30, 2013·Database : the Journal of Biological Databases and Curation·Juergen HaasTorsten Schwede
Dec 8, 2009·Nucleic Acids Research·Marcel ThönAxel A Brakhage
May 12, 2009·Nucleic Acids Research·Pascal BenkertTorsten Schwede
Jun 16, 2012·Biology of Reproduction·Erick J R SilvaMichael G O'Rand
Apr 25, 2012·Acta Crystallographica. Section D, Biological Crystallography·Eugenio De la MoraEnrique Rudino-Pinera
Jul 14, 2010·Journal of Gastroenterology and Hepatology·Juntaro MatsuzakiToshifumi Hibi
Aug 17, 2010·FEMS Yeast Research·Niran RoongsawangSutipa Tanapongpipat
Sep 29, 2011·Antimicrobial Agents and Chemotherapy·Edwin KamauJon Boyle
Oct 17, 2012·Antimicrobial Agents and Chemotherapy·Yong Heon LeeJohn D Helmann
Oct 5, 2010·Applied and Environmental Microbiology·Fernando López-GallegoClaudia Schmidt-Dannert
Aug 2, 2011·Applied and Environmental Microbiology·Jef Van der BorghtWim Soetaert

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