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The Protein Model Portal
Project funded by own resources
Project title The Protein Model Portal
Principal Investigator(s) Schwede, Torsten
Project Members Bordoli, Lorenza
Arnold, Konstantin
Haas, Jürgen
Roth, Steven
Barbato, Alessandro
Waterhouse, Andrew
Organisation / Research unit Departement Biozentrum / Bioinformatics (Schwede)
Project Website http://www.proteinmodelportal.org
Project start 01.04.2007
Probable end 31.07.2016
Status Completed
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. The PSI SGKB Protein Model Portal was supported by the National Institutes of Health NIH as a sub-grant with Fox Chase Cancer Center grant 3 P20 GM076222-02S1, and as a sub-grant with Rutgers University, under Prime Agreement Award Number: 3U54GM074958-04S2.

Keywords PSI, Protein Structure Modeling, Structural Genomics
Financed by Other funds

Published results ()

  ID Autor(en) Titel ISSN / ISBN Erschienen in Art der Publikation
156359  Arnold, K.; Kiefer, F.; Kopp, J.; Battey, J.N.; Podvinec, M.; Westbrook, J.D.; Berman, H.M.; Bordoli, L.; Schwede, T.  The Protein Model Portal  1345-711X  Journal of Structural and Functional Genomics  Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) 
156360  Berman, H.M.; Westbrook, J.D.; Gabanyi, M.J.; Tao, W.; Shah, R.; Kouranov, A.; Schwede, T.; Arnold, K.; Kiefer, F.; Bordoli, L.; Kopp, J.; Podvinec, M.; Adams, P.D.; Carter, L.G.; Minor, W.; Nair, R.; Baer, J.L.  The protein structure initiative structural genomics knowledgebase  1362-4962  Nucleic Acids Research  Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) 
749242  Gabanyi, Margaret J; Adams, Paul D; Arnold, Konstantin; Bordoli, Lorenza; Carter, Lester G; Flippen-Andersen, Judith; Gifford, Lida; Haas, Juergen; Kouranov, Andrei; McLaughlin, William A; Micallef, David I; Minor, Wladek; Shah, Raship; Schwede, Torsten; Tao, Yi-Ping; Westbrook, John D; Zimmerman, Matthew; Berman, Helen M  The Structural Biology Knowledgebase : a portal to protein structures, sequences, functions, and methods  1345-711x  Journal of structural and functional genomics  Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) 
1772202  Haas, Juergen; Roth, Steven; Arnold, Konstantin; Kiefer, Florian; Schmidt, Tobias; Bordoli, Lorenza; Schwede, Torsten  The Protein Model Portal: a comprehensive resource for protein structure and model information    Database  Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) 
2158293  Schwede, Torsten  Protein modeling: what happened to the "protein structure gap"?  0969-2126  Structure: with folding and design  Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) 
156321  Arnold, K.; Kiefer, F.; Kopp, J.; Battey, J. N.; Podvinec, M.; Westbrook, J. D.; Berman, H. M.; Bordoli, L.; Schwede, T.  The protein model portal  1345-711x  Journal of structural and functional genomics  Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) 
156322  Berman, H. M.; Westbrook, J. D.; Gabanyi, M. J.; Tao, W.; Shah, R.; Kouranov, A.; Schwede, T.; Arnold, K.; Kiefer, F.; Bordoli, L.; Kopp, J.; Podvinec, M.; Adams, P. D.; Carter, L. G.; Minor, W.; Nair, R.; Baer, J. L.  The protein structure initiative structural genomics knowledgebase  0305-1048 ; 1362-4962  Nucleic Acids Research  Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) 
156344  Schwede, T.; Sali, A.; Eswar, N.; Peitsch, M. C.  Protein Structure Modeling  978-981-277-877-2 (hardcover : alk. paper) ; 981-277-877-2 (hardcover : alk. paper)  Computational structural biology  Publication: Book Item (Buchkap., Lexikonartikel, jur. Kommentierung, Beiträge in Sammelbänden etc.) 
156357  Schwede, Torsten; Sali, Andrej; Honig, Barry; Levitt, Michael; Berman, Helen M; Jones, David; Brenner, Steven E; Burley, Stephen K; Das, Rhiju; Dokholyan, Nikolay V; Dunbrack, Roland L; Fidelis, Krzysztof; Fiser, Andras; Godzik, Adam; Huang, Yuanpeng Janet; Humblet, Christine; Jacobson, Matthew P; Joachimiak, Andrzej; Krystek, Stanley R; Kortemme, Tanja; Kryshtafovych, Andriy; Montelione, Gaetano T; Moult, John; Murray, Diana; Sanchez, Roberto; Sosnick, Tobin R; Standley, Daron M; Stouch, Terry; Vajda, Sandor; Vasquez, Max; Westbrook, John D; Wilson, Ian A  Outcome of a workshop on applications of protein models in biomedical research  0969-2126  Structure  Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) 
1889551  Trewhella, Jill; Hendrickson, Wayne A; Kleywegt, Gerard J; Sali, Andrej; Sato, Mamoru; Schwede, Torsten; Svergun, Dmitri I; Tainer, John A; Westbrook, John; Berman, Helen M  Report of the wwPDB Small-Angle Scattering Task Force : data requirements for biomolecular modeling and the PDB  0969-2126  Structure: with folding and design  JournalItem (Kommentare, Editorials, Rezensionen, Urteilsanmerk., etc. in einer wissensch. Zeitschr. 
2816480  Berman, Helen M; Gabanyi, Margaret J; Groom, Colin R; Johnson, John E; Murshudov, Garib N; Nicholls, Robert A; Reddy, Vijay; Schwede, Torsten; Zimmerman, Matthew D; Westbrook, John; Minor, Wladek  Data to knowledge: how to get meaning from your result    IUCrJ  Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) 
3165865  Sali, Andrej; Berman, Helen M.; Schwede, Torsten; Trewhella, Jill; Kleywegt, Gerard; Burley, Stephen K.; Markley, John; Nakamura, Haruki; Adams, Paul; Bonvin, Alexandre M. J. J.; Chiu, Wah; Peraro, Matteo Dal; Di Maio, Frank; Ferrin, Thomas E.; Grünewald, Kay; Gutmanas, Aleksandras; Henderson, Richard; Hummer, Gerhard; Iwasaki, Kenji; Johnson, Graham; Lawson, Catherine L.; Meiler, Jens; Marti-Renom, Marc A.; Montelione, Gaetano T.; Nilges, Michael; Nussinov, Ruth; Patwardhan, Ardan; Rappsilber, Juri; Read, Randy J.; Saibil, Helen; Schröder, Gunnar F.; Schwieters, Charles D.; Seidel, Claus A. M.; Svergun, Dmitri; Topf, Maya; Ulrich, Eldon L.; Velankar, Sameer; Westbrook, John D.  Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop  0969-2126  Structure: with folding and design  Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) 

Cooperations ()

  ID Kreditinhaber Kooperationspartner Institution Laufzeit - von Laufzeit - bis
105119  Schwede, Torsten  Berman, Helen  RCSB PDB, Nature PSI Structural Genomics Knowledgebase  01.04.2007  31.12.2017 
105129  Schwede, Torsten  Westbrook, John D.  RCSB PDB, Nature PSI Structural Genomics Knowledgebase   01.04.2007  31.07.2016 
3721744  Schwede, Torsten  Sali, Andrej  UCSF, University of San Francisco, CA  01.01.2012  31.12.2017 
   

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