The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling - PubMed (original) (raw)

. 2006 Jan 15;22(2):195-201.

doi: 10.1093/bioinformatics/bti770. Epub 2005 Nov 13.

Affiliations

• PMID: 16301204
• DOI: 10.1093/bioinformatics/bti770

The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling

Konstantin Arnold et al. Bioinformatics. 2006.

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/

PubMed Disclaimer

Similar articles

• A web-based three-dimensional protein retrieval system by matching visual similarity.
  Yeh JS, Chen DY, Chen BY, Ouhyoung M. Yeh JS, et al. Bioinformatics. 2005 Jul 1;21(13):3056-7. doi: 10.1093/bioinformatics/bti458. Epub 2005 Apr 19. Bioinformatics. 2005. PMID: 15840701
• MAGOS: multiple alignment and modelling server.
  Garnier N, Friedrich A, Bolze R, Bettler E, Moulinier L, Geourjon C, Thompson JD, Deléage G, Poch O. Garnier N, et al. Bioinformatics. 2006 Sep 1;22(17):2164-5. doi: 10.1093/bioinformatics/btl349. Epub 2006 Jul 4. Bioinformatics. 2006. PMID: 16820425
• ExPASy: The proteomics server for in-depth protein knowledge and analysis.
  Gasteiger E, Gattiker A, Hoogland C, Ivanyi I, Appel RD, Bairoch A. Gasteiger E, et al. Nucleic Acids Res. 2003 Jul 1;31(13):3784-8. doi: 10.1093/nar/gkg563. Nucleic Acids Res. 2003. PMID: 12824418 Free PMC article.
• Five hierarchical levels of sequence-structure correlation in proteins.
  Bystroff C, Shao Y, Yuan X. Bystroff C, et al. Appl Bioinformatics. 2004;3(2-3):97-104. doi: 10.2165/00822942-200403020-00004. Appl Bioinformatics. 2004. PMID: 15693735 Review.
• Protein structure computing in the genomic era.
  Schwede T, Diemand A, Guex N, Peitsch MC. Schwede T, et al. Res Microbiol. 2000 Mar;151(2):107-12. doi: 10.1016/s0923-2508(00)00121-2. Res Microbiol. 2000. PMID: 10865955 Review.

Cited by

• Comprehensive analysis of PLATZ family genes and their responses to abiotic stresses in Barley.
  Feng X, Zhu G, Meng Q, Zeng J, He X, Liu W. Feng X, et al. BMC Plant Biol. 2024 Oct 18;24(1):982. doi: 10.1186/s12870-024-05690-5. BMC Plant Biol. 2024. PMID: 39420254 Free PMC article.
• Case report: Multiple facial trichoepitheliomas caused by p.Val835SerfsTer52 variant of CYLD gene.
  Gaydina TA, Patsap OI, Buianova AA. Gaydina TA, et al. Front Med (Lausanne). 2024 Sep 30;11:1458723. doi: 10.3389/fmed.2024.1458723. eCollection 2024. Front Med (Lausanne). 2024. PMID: 39403278 Free PMC article.
• The Phylogenomic Characterization of Planotetraspora Species and Their Cellulases for Biotechnological Applications.
  Bouras N, Bakli M, Dif G, Smaoui S, Șmuleac L, Paşcalău R, Menendez E, Nouioui I. Bouras N, et al. Genes (Basel). 2024 Sep 12;15(9):1202. doi: 10.3390/genes15091202. Genes (Basel). 2024. PMID: 39336793 Free PMC article.
• Enhancing the imidase activity of BpIH toward 3-isobutyl glutarimide via semi-rational design.
  Qin W, Xu L, Cheng K, Lu Y, Yang Z. Qin W, et al. Appl Microbiol Biotechnol. 2024 Sep 25;108(1):474. doi: 10.1007/s00253-024-13311-2. Appl Microbiol Biotechnol. 2024. PMID: 39320489 Free PMC article.
• In silico characterization and homology modeling of Nile tilapia (Oreochromis niloticus) Hsp70cBi and Hsp70cBc proteins.
  Dayrit GB, Burigsay NPF, Vera Cruz EM, Santos MD. Dayrit GB, et al. Heliyon. 2024 Jun 8;10(12):e32748. doi: 10.1016/j.heliyon.2024.e32748. eCollection 2024 Jun 30. Heliyon. 2024. PMID: 39183877 Free PMC article.

Publication types

MeSH terms

Substances

LinkOut - more resources

• Full Text Sources

  • Ovid Technologies, Inc.
  • Silverchair Information Systems

• Other Literature Sources

  • The Lens - Patent Citations Database