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Arnold K, Kiefer F, Kopp J, Battey JND, Podvinec M, Westbrook JD, Berman HM, Bordoli L, Schwede T. The Protein Model Portal. JOURNAL OF STRUCTURAL AND FUNCTIONAL GENOMICS 2009; 10:1-8. [PMID: 19037750 PMCID: PMC2704613 DOI: 10.1007/s10969-008-9048-5] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2008] [Accepted: 11/02/2008] [Indexed: 11/28/2022]
Abstract
Structural Genomics has been successful in determining the structures of many unique proteins in a high throughput manner. Still, the number of known protein sequences is much larger than the number of experimentally solved protein structures. Homology (or comparative) modeling methods make use of experimental protein structures to build models for evolutionary related proteins. Thereby, experimental structure determination efforts and homology modeling complement each other in the exploration of the protein structure space. One of the challenges in using model information effectively has been to access all models available for a specific protein in heterogeneous formats at different sites using various incompatible accession code systems. Often, structure models for hundreds of proteins can be derived from a given experimentally determined structure, using a variety of established methods. This has been done by all of the PSI centers, and by various independent modeling groups. The goal of the Protein Model Portal (PMP) is to provide a single portal which gives access to the various models that can be leveraged from PSI targets and other experimental protein structures. A single interface allows all existing pre-computed models across these various sites to be queried simultaneously, and provides links to interactive services for template selection, target-template alignment, model building, and quality assessment. The current release of the portal consists of 7.6 million model structures provided by different partner resources (CSMP, JCSG, MCSG, NESG, NYSGXRC, JCMM, ModBase, SWISS-MODEL Repository). The PMP is available at http://www.proteinmodelportal.org and from the PSI Structural Genomics Knowledgebase.
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Affiliation(s)
- Konstantin Arnold
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
- Swiss Institute of Bioinformatics (SIB), Basel, Switzerland
| | - Florian Kiefer
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
- Swiss Institute of Bioinformatics (SIB), Basel, Switzerland
| | - Jürgen Kopp
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
- Swiss Institute of Bioinformatics (SIB), Basel, Switzerland
| | - James N. D. Battey
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
- Swiss Institute of Bioinformatics (SIB), Basel, Switzerland
| | - Michael Podvinec
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
- Swiss Institute of Bioinformatics (SIB), Basel, Switzerland
| | - John D. Westbrook
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854-8087 USA
| | - Helen M. Berman
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854-8087 USA
| | - Lorenza Bordoli
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
- Swiss Institute of Bioinformatics (SIB), Basel, Switzerland
| | - Torsten Schwede
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
- Swiss Institute of Bioinformatics (SIB), Basel, Switzerland
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Schwede T, Sali A, Honig B, Levitt M, Berman HM, Jones D, Brenner SE, Burley SK, Das R, Dokholyan NV, Dunbrack RL, Fidelis K, Fiser A, Godzik A, Huang YJ, Humblet C, Jacobson MP, Joachimiak A, Krystek SR, Kortemme T, Kryshtafovych A, Montelione GT, Moult J, Murray D, Sanchez R, Sosnick TR, Standley DM, Stouch T, Vajda S, Vasquez M, Westbrook JD, Wilson IA. Outcome of a workshop on applications of protein models in biomedical research. Structure 2009; 17:151-9. [PMID: 19217386 PMCID: PMC2739730 DOI: 10.1016/j.str.2008.12.014] [Citation(s) in RCA: 120] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2008] [Revised: 11/14/2008] [Accepted: 12/16/2008] [Indexed: 02/05/2023]
Abstract
We describe the proceedings and conclusions from the "Workshop on Applications of Protein Models in Biomedical Research" (the Workshop) that was held at the University of California, San Francisco on 11 and 12 July, 2008. At the Workshop, international scientists involved with structure modeling explored (i) how models are currently used in biomedical research, (ii) the requirements and challenges for different applications, and (iii) how the interaction between the computational and experimental research communities could be strengthened to advance the field.
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Affiliation(s)
- Torsten Schwede
- Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Klingelbergstrasse 50-70, CH-4056 Basel, Switzerland.
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Kiefer F, Arnold K, Künzli M, Bordoli L, Schwede T. The SWISS-MODEL Repository and associated resources. Nucleic Acids Res 2009; 37:D387-92. [PMID: 18931379 PMCID: PMC2686475 DOI: 10.1093/nar/gkn750] [Citation(s) in RCA: 1587] [Impact Index Per Article: 99.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2008] [Accepted: 10/05/2008] [Indexed: 12/12/2022] Open
Abstract
SWISS-MODEL Repository (http://swissmodel.expasy.org/repository/) is a database of 3D protein structure models generated by the SWISS-MODEL homology-modelling pipeline. The aim of the SWISS-MODEL Repository is to provide access to an up-to-date collection of annotated 3D protein models generated by automated homology modelling for all sequences in Swiss-Prot and for relevant models organisms. Regular updates ensure that target coverage is complete, that models are built using the most recent sequence and template structure databases, and that improvements in the underlying modelling pipeline are fully utilised. As of September 2008, the database contains 3.4 million entries for 2.7 million different protein sequences from the UniProt database. SWISS-MODEL Repository allows the users to assess the quality of the models in the database, search for alternative template structures, and to build models interactively via SWISS-MODEL Workspace (http://swissmodel.expasy.org/workspace/). Annotation of models with functional information and cross-linking with other databases such as the Protein Model Portal (http://www.proteinmodelportal.org) of the PSI Structural Genomics Knowledge Base facilitates the navigation between protein sequence and structure resources.
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Affiliation(s)
- Florian Kiefer
- Biozentrum, University of Basel and SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Konstantin Arnold
- Biozentrum, University of Basel and SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Michael Künzli
- Biozentrum, University of Basel and SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Lorenza Bordoli
- Biozentrum, University of Basel and SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Torsten Schwede
- Biozentrum, University of Basel and SIB Swiss Institute of Bioinformatics, Basel, Switzerland
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Berman HM, Westbrook JD, Gabanyi MJ, Tao W, Shah R, Kouranov A, Schwede T, Arnold K, Kiefer F, Bordoli L, Kopp J, Podvinec M, Adams PD, Carter LG, Minor W, Nair R, La Baer J. The protein structure initiative structural genomics knowledgebase. Nucleic Acids Res 2009; 37:D365-8. [PMID: 19010965 PMCID: PMC2686438 DOI: 10.1093/nar/gkn790] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2008] [Accepted: 10/08/2008] [Indexed: 11/13/2022] Open
Abstract
The Protein Structure Initiative Structural Genomics Knowledgebase (PSI SGKB, http://kb.psi-structuralgenomics.org) has been created to turn the products of the PSI structural genomics effort into knowledge that can be used by the biological research community to understand living systems and disease. This resource provides central access to structures in the Protein Data Bank (PDB), along with functional annotations, associated homology models, worldwide protein target tracking information, available protocols and the potential to obtain DNA materials for many of the targets. It also offers the ability to search all of the structural and methodological publications and the innovative technologies that were catalyzed by the PSI's high-throughput research efforts. In collaboration with the Nature Publishing Group, the PSI SGKB provides a research library, editorials about new research advances, news and an events calendar to present a broader view of structural biology and structural genomics. By making these resources freely available, the PSI SGKB serves as a bridge to connect the structural biology and the greater biomedical communities.
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Affiliation(s)
- Helen M Berman
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
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Future structural genomics initiatives: an interview with Helen Berman, director of the Protein Data Bank. Interview by Wendy A Warr. J Comput Aided Mol Des 2008; 22:707-10. [PMID: 18781281 DOI: 10.1007/s10822-008-9234-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2008] [Accepted: 08/08/2008] [Indexed: 10/21/2022]
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