The Protein Model Portal

Journal of Structural and Functional Genomics

Volumn 10, Issue 1, 2009, Pages 1-8

  Arnold, Konstantin ^a,b   Kiefer, Florian ^a,b   Kopp, Jürgen ^a,b   Battey, James N D ^a,b   Podvinec, Michael ^a,b   Westbrook, John D ^c   Berman, Helen M ^c   Bordoli, Lorenza ^a,b   Schwede, Torsten ^b  

^a UNIVERSITY OF BASEL   (Switzerland)

^b SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

^c RUTGERS UNIVERSITY   (United States)

Author keywords

Comparative protein structure modeling; Homology modeling; Model database; Protein model portal; PSI structural genomics knowledgebase

Indexed keywords

DATA BASE; HIGH THROUGHPUT SCREENING; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN STRUCTURE; REVIEW; SEQUENCE HOMOLOGY; STRUCTURAL GENOMICS; STRUCTURE ANALYSIS;

AMINO ACID SEQUENCE; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; HUMANS; INTERNET; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEINS; SEQUENCE ALIGNMENT; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 60849113411     PISSN: 1345711X     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10969-008-9048-5     Document Type: Review

References (33)

1. H Berman 2007 The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data Nucleic Acids Res 35 D301 D303 10.1093/nar/gkl971
2. S Yooseph 2007 The sorcerer II global ocean sampling expedition: expanding the universe of protein families PLoS Biol 5 e16 10.1371/journal.pbio. 0050016
3. D Baker A Sali 2001 Protein structure prediction and structural genomics Science 294 93 96 10.1126/science.1065659
4. A Hillisch LF Pineda R Hilgenfeld 2004 Utility of homology models in the drug discovery process Drug Discov Today 9 659 669 10.1016/S1359-6446(04)03196-4
5. MC Peitsch 2002 About the use of protein models Bioinformatics 18 934 938 10.1093/bioinformatics/18.7.934
6. A Tramontano 2008
7. HM Berman 2008 Harnessing knowledge from structural genomics Structure 16 16 18 10.1016/j.str.2007.12.003
8. Berman HM et al (2008) The protein structure initiative structural genomics knowledgebase. Nucleic Acids Res. Database Issue (in press)
9. H Berman K Henrick H Nakamura 2003 Announcing the worldwide Protein Data Bank Nat Struct Biol 10 980 10.1038/nsb1203-980
10. U Pieper 2006 MODBASE: a database of annotated comparative protein structure models and associated resources Nucleic Acids Res 34 D291 D295 10.1093/nar/gkj059
11. T Schwede 2003 SWISS-MODEL: an automated protein homology-modeling server Nucleic Acids Res 31 3381 3385 10.1093/nar/gkg520
12. C Yeats 2006 Gene3D: modelling protein structure, function and evolution Nucleic Acids Res 34 D281 D284 10.1093/nar/gkj057
13. N Mirkovic 2007 Strategies for high-throughput comparative modeling: applications to leverage analysis in structural genomics and protein family organization Proteins 66 766 777 10.1002/prot.21191
14. T Schwede 2008
15. Y Zhang 2007 Template-based modeling and free modeling by I-TASSER in CASP7 Proteins 69 Suppl 8 108 117 10.1002/prot.21702
16. D Chivian D Baker 2006 Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection Nucleic Acids Res 34 e112 10.1093/nar/gkl480
17. A Bairoch 2005 The universal protein resource (UniProt) Nucleic Acids Res 33 D154 D159 10.1093/nar/gki070
18. Mulder NJ, Apweiler R (2008) The InterPro database and tools for protein domain analysis. Curr Protoc Bioinformatics. Chapter 2:Unit 2.7
19. JN Battey 2007 Automated server predictions in CASP7 Proteins 69 Suppl 8 68 82 10.1002/prot.21761
20. J Kopp 2007 Assessment of CASP7 predictions for template-based modeling targets Proteins 69 Suppl 8 38 56 10.1002/prot.21753
21. HM Berman 2006 Outcome of a workshop on archiving structural models of biological macromolecules Structure 14 1211 1217 10.1016/j.str.2006.06.005
22. J Kopp T Schwede 2004 The SWISS-MODEL repository of annotated three-dimensional protein structure homology models Nucleic Acids Res 32 D230 D234 10.1093/nar/gkh008
23. J Kopp T Schwede 2006 The SWISS-MODEL repository: new features and functionalities Nucleic Acids Res 34 D315 D318 10.1093/nar/gkj056
24. SF Altschul 1997 Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucleic Acids Res 25 3389 3402 10.1093/nar/25.17.3389
25. H Huang 2007 Integration of bioinformatics resources for functional analysis of gene expression and proteomic data Front Biosci 12 5071 5088 10.2741/2449
26. AM Jenkinson 2008 Integrating biological data-the Distributed Annotation System BMC Bioinformatics 9 Suppl 8 S3 10.1186/1471-2105-9-S8-S3
27. PJ Kraulis 1991 MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures J Appl Crystallogr 24 946 950
28. EA Merritt ME Murphy 1994 Raster3D Version 2.0. A program for photorealistic molecular graphics Acta Crystallogr D Biol Crystallogr 50 869 873 10.1107/S0907444994006396
29. AR Ortiz CE Strauss O Olmea 2002 MAMMOTH (matching molecular models obtained from theory): an automated method for model comparison Protein Sci 11 2606 2621 10.1110/ps.0215902
30. MJ Hartshorn 2002 AstexViewer: a visualisation aid for structure-based drug design J Comput Aided Mol Des 16 871 881 10.1023/A:1023813504011
31. RD Finn 2008 The Pfam protein families database Nucleic Acids Res 36 D281 D288 10.1093/nar/gkm960
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