The Protein Model Portal

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• 作者：Konstantin Arnold (1) (2)
  Florian Kiefer (1) (2)
  Jürgen Kopp (1) (2)
  James N. D. Battey (1) (2)
  Michael Podvinec (1) (2)
  John D. Westbrook (3)
  Helen M. Berman (3)
  Lorenza Bordoli (1) (2)
  Torsten Schwede (1) (2)
  
• 关键词：Protein model portal ; PSI structural genomics knowledgebase ; Comparative protein structure modeling ; Homology modeling ; Model database
• 刊名：Journal of Structural and Functional Genomics
• 出版年：2009
• 出版时间：March 2009
• 年：2009
• 卷：10
• 期：1
• 页码：1-8
• 全文大小：918KB
• 参考文献：1. Berman H et al (2007) The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res 35:D301–D303. doi:10.1093/nar/gkl971 CrossRef
  2. Yooseph S et al (2007) The sorcerer II global ocean sampling expedition: expanding the universe of protein families. PLoS Biol 5:e16. doi:10.1371/journal.pbio.0050016 CrossRef
  3. Baker D, Sali A (2001) Protein structure prediction and structural genomics. Science 294:93-6. doi:10.1126/science.1065659 CrossRef
  4. Hillisch A, Pineda LF, Hilgenfeld R (2004) Utility of homology models in the drug discovery process. Drug Discov Today 9:659-69. doi:10.1016/S1359-6446(04)03196-4 CrossRef
  5. Peitsch MC (2002) About the use of protein models. Bioinformatics 18:934-38. doi:10.1093/bioinformatics/18.7.934 CrossRef
  6. Tramontano A (2008) The biological applications of protein models. In: Schwede T, Peitsch MC (eds) Computational structural biology. World Scientific Publishing, Singapore
  7. Berman HM (2008) Harnessing knowledge from structural genomics. Structure?16:16-8. doi:10.1016/j.str.2007.12.003 CrossRef
  8. Berman HM et?al (2008) The protein structure initiative structural genomics knowledgebase. Nucleic Acids Res. Database Issue (in press)
  9. Berman H, Henrick K, Nakamura H (2003) Announcing the worldwide Protein Data Bank. Nat Struct Biol 10:980. doi:10.1038/nsb1203-980 CrossRef
  10. Pieper U et al (2006) MODBASE: a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res 34:D291–D295. doi:10.1093/nar/gkj059 CrossRef
  11. Schwede T et al (2003) SWISS-MODEL: an automated protein homology-modeling server. Nucleic Acids Res 31:3381-385. doi:10.1093/nar/gkg520 CrossRef
  12. Yeats C et al (2006) Gene3D: modelling protein structure, function and evolution. Nucleic Acids Res 34:D281–D284. doi:10.1093/nar/gkj057 CrossRef
  13. Mirkovic N et al (2007) Strategies for high-throughput comparative modeling: applications to leverage analysis in structural genomics and protein family organization. Proteins 66:766-77. doi:10.1002/prot.21191 CrossRef
  14. Schwede T et al (2008) Protein structure modeling. In: Schwede T, Peitsch MC (eds) Computational structural biology. World Scientific Publishing, Singapore
  15. Zhang Y (2007) Template-based modeling and free modeling by I-TASSER in CASP7. Proteins 69(Suppl 8):108-17. doi:10.1002/prot.21702 CrossRef
  16. Chivian D, Baker D (2006) Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection. Nucleic Acids Res 34:e112. doi:10.1093/nar/gkl480 CrossRef
  17. Bairoch A et al (2005) The universal protein resource (UniProt). Nucleic Acids Res 33:D154–D159. doi:10.1093/nar/gki070 CrossRef
  18. Mulder NJ, Apweiler R (2008) The InterPro database and tools for protein domain analysis / . Curr Protoc Bioinformatics. Chapter 2:Unit 2.7
  19. Battey JN et al (2007) Automated server predictions in CASP7. Proteins 69(Suppl 8):68-2. doi:10.1002/prot.21761 CrossRef
  20. Kopp J et al (2007) Assessment of CASP7 predictions for template-based modeling targets. Proteins 69(Suppl 8):38-6. doi:10.1002/prot.21753 CrossRef
  21. Berman HM et al (2006) Outcome of a workshop on archiving structural models of biological macromolecules. Structure?14:1211-217. doi:10.1016/j.str.2006.06.005 CrossRef
  22. Kopp J, Schwede T (2004) The SWISS-MODEL repository of annotated three-dimensional protein structure homology models. Nucleic Acids Res 32:D230–D234. doi:10.1093/nar/gkh008 CrossRef
  23. Kopp J, Schwede T (2006) The SWISS-MODEL repository: new features and functionalities. Nucleic Acids Res 34:D315–D318. doi:10.1093/nar/gkj056 CrossRef
  24. Altschul SF et al (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389-402. doi:10.1093/nar/25.17.3389 CrossRef
  25. Huang H et al (2007) Integration of bioinformatics resources for functional analysis of gene expression and proteomic data. Front Biosci 12:5071-088. doi:10.2741/2449 CrossRef
  26. Jenkinson AM et al (2008) Integrating biological data—the Distributed Annotation System. BMC Bioinformatics 9(Suppl 8):S3. doi:10.1186/1471-2105-9-S8-S3 CrossRef
  27. Kraulis PJ (1991) MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J Appl Crystallogr 24:946-50 CrossRef
  28. Merritt EA, Murphy ME (1994) Raster3D Version 2.0. A program for photorealistic molecular graphics. Acta Crystallogr D Biol Crystallogr 50:869-73. doi:10.1107/S0907444994006396 CrossRef
  29. Ortiz AR, Strauss CE, Olmea O (2002) MAMMOTH (matching molecular models obtained from theory): an automated method for model comparison. Protein Sci 11:2606-621. doi:10.1110/ps.0215902 CrossRef
  30. Hartshorn MJ (2002) AstexViewer: a visualisation aid for structure-based drug design. J Comput Aided Mol Des 16:871-81. doi:10.1023/A:1023813504011 CrossRef
  31. Finn RD et al (2008) The Pfam protein families database. Nucleic Acids Res 36:D281–D288. doi:10.1093/nar/gkm960 CrossRef
  32. Pieper U et?al (2008) MODBASE, a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res. doi:10.1093/nar/gkn791
  33. Kiefer F et?al (2008) The SWISS-MODEL Repository and associated resources. Nucleic Acids Res. doi:10.1093/nar/gkn750
  
• 作者单位：Konstantin Arnold (1) (2)
  Florian Kiefer (1) (2)
  Jürgen Kopp (1) (2)
  James N. D. Battey (1) (2)
  Michael Podvinec (1) (2)
  John D. Westbrook (3)
  Helen M. Berman (3)
  Lorenza Bordoli (1) (2)
  Torsten Schwede (1) (2)
  
  1. Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056, Basel, Switzerland
  2. Swiss Institute of Bioinformatics (SIB), Basel, Switzerland
  3. Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854-8087, USA
  

文摘

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.