Protein structure prediction on the web: A case study using the phyre server

Nature Protocols

Volumn 4, Issue 3, 2009, Pages 363-373

  Kelley, Lawrence A ^a   Sternberg, Michael J E ^a  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIOLOGY; CHEMICAL STRUCTURE; GENE DELETION; GENE EXPRESSION REGULATION; INTERNET; METHODOLOGY; POINT MUTATION; PROTEIN CONFORMATION;

COMPUTATIONAL BIOLOGY; INTERNET; MODELS, MOLECULAR; MUTAGENESIS, INSERTIONAL; POINT MUTATION; PROTEIN CONFORMATION; SEQUENCE DELETION;

EID: 63849246525     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2009.2     Document Type: Article

References (28)

1. CASP 7 special issue. Proteins 69 (Suppl. 8), 1-207 (2007).
2. Baker, D. & Sali, A. Protein structure prediction and structural genomics. Science 294, 93-96 (2001).
3. Watson, J.D., Laskowski, R.A. & Thornton, J.M. Predicting protein function from sequence and structural data. Curr. Opin. Struct. Biol. 15, 275-284 (2005).
4. Qian, B. et al. High-resolution structure prediction and the crystallographic phase problem. Nature 450, 259-264 (2007).
5. Rava, P. & Hussain, M.M. Acquisition of triacylglycerol transfer activity by microsomal triglyceride transfer protein during evolution. Biochemistry 46, 12263-12274 (2007).
6. Park, H. et al. Discoveryofnovelalpha-glucosidaseinhibitorsbasedonthevirtual screening with the homology-modeled protein structure. Bioorg. Med. Chem. 16, 284-292 (2008).
7. Altschul, S.F. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402 (1997).
8. Karplus, K., Barrett, C. & Hughey, R. Hidden Markov models for detecting remote protein homologies. Bioinformatics 14, 846-856 (1998).
9. Ohlson, T., Wallner, B. & Elofsson, A. Profile-profile methods provide improved fold-recognition: a study of different profile-profile alignment methods. Proteins 57, 188-197 (2004).
10. Bennett-Lovsey, R.M., Herbert, A.D., Sternberg, M.J.E. & Kelley, L.A. Exploring the extremes of sequence/structure space with ensemble fold recognition in the program Phyre. Proteins 70, 611-625 (2008).
11. Murzin, A.G., Brenner, S.E., Hubbard, T. & chothia, C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247, 536-540 (1995).
12. Berman, H.M. et al. The protein data bank. Nucleic Acids Res. 28, 235-242 (2000).
13. McGuffin, L.J., Bryson, K. & Jones, D.T. The PSIPRED protein structure prediction server. Bioinformatics 16, 404-405 (2000).
14. Pollastri, G., Przybylski, D., Rost, B. & Baldi, P. Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles. Proteins 47, 228-235 (2002).
15. Cole, C., Barber, J.D. & Barton, G.J. The Jpred 3 secondary structure prediction server. Nucleic Acids Res. 36 (Web server issue): W197-W201 (2008).
16. Ward, J.J., McGuffin, L.J., Bryson, K., Buxton, B.F. & Jones, D.T. The DISOPRED server for the prediction of protein disorder. Bioinformatics 20, 2138-2139 (2004).
17. Tress, M.L., Jones, D.T. & Valenica, A. Predicting reliable regions in protein alignments from sequence profiles. J. Mol. Biol. 330, 705-718 (2003).
18. Marchler-Bauer, A. et al. CDD: a conserved domain database for interactive domain family analysis. Nucleic Acids Res. 35 (Database issue): D237-D240 (2007).
19. Finn, R.D. et al. The Pfam protein families database. Nucleic Acids Res. 36 (Database issue): D281-D288 (2008).
20. Wass, M.N. & Sternberg, M.J.E. ConFunc—functional annotation in the twilight zone. Bioinformatics 24, 798-806 (2008).
21. Yao, H. et al. An accurate, sensitive, and scalable method to identify functional sites in protein structures. J. Mol. Biol. 326, 255-261 (2003).
22. Kinoshita, K. & Nakamura, H. Identification of protein biochemical functions by similarity search using the molecular surface database eF-site. Protein Sci. 12, 1589-1595 (2003).
23. Laskowski, R.A. et al. Protein clefts in molecular recognition and function. Prot. Sci. 5, 2438-2452 (1996).
24. Liang, J., Edelsbrunner, H., Fu, P., Sudhakar, P.V. & Subramaniam, S. Analytical shape computation of macromolecules I and II. Proteins 33, 1-17 and 18-29 (1998).
25. Jones, D.T. Predicting novel protein folds by using FRAGFOLD. Proteins 45 (Suppl. 5): 127-132 (2001).
26. Kim, D.E., Chivian, D. & Baker, D. Protein structure prediction and analysis using the Robetta server. Nucleic Acids Res. 32 (Web server issue): W526-W531 (2004).
27. Zhang, Y. Template-based modeling and free modeling by I-TASSER in CASP7. Proteins 69 (Suppl. 8): 108-117 (2007).
28. Hulo, N. et al. The 20 years of PROSITE. Nucleic Acids Res. 36 (Database issue): D245-D249 (2008).