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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
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Published results () |
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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) |
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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) |
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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 |
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Database |
Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) |
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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) |
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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) |
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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.) |
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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) |
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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. |
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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 |
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IUCrJ |
Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) |
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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) |
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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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