Protein structure prediction on the Web: a case study using the Phyre server

Nature Protocols - Tập 4 Số 3 - Trang 363-371 - 2009
Lawrence A. Kelley1, Michael J.E. Sternberg2
1Structural Bioinformatics Group, Division of Molecular Biosciences, Department of Life Sciences, Imperial College London, South Kensington Campus, London, UK
2Division of Molecular Biosciences, Department of Life Sciences, Structural Bioinformatics Group, Imperial College London, South Kensington Campus, London, UK

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CASP 7 special issue. Proteins 69 (Suppl. 8), 1–207 (2007).

Baker, D. & Sali, A. Protein structure prediction and structural genomics. Science 294, 93–96 (2001).

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).

Qian, B. et al. High-resolution structure prediction and the crystallographic phase problem. Nature 450, 259–264 (2007).

Rava, P. & Hussain, M.M. Acquisition of triacylglycerol transfer activity by microsomal triglyceride transfer protein during evolution. Biochemistry 46, 12263–12274 (2007).

Park, H. et al. Discovery of novel alpha-glucosidase inhibitors based on the virtual screening with the homology-modeled protein structure. Bioorg. Med. Chem. 16, 284–292 (2008).

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).

Karplus, K., Barrett, C. & Hughey, R. Hidden Markov models for detecting remote protein homologies. Bioinformatics 14, 846–856 (1998).

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).

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).

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).

Berman, H.M. et al. The protein data bank. Nucleic Acids Res. 28, 235–242 (2000).

McGuffin, L.J., Bryson, K. & Jones, D.T. The PSIPRED protein structure prediction server. Bioinformatics 16, 404–405 (2000).

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).

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).

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).

Tress, M.L., Jones, D.T. & Valenica, A. Predicting reliable regions in protein alignments from sequence profiles. J. Mol. Biol. 330, 705–718 (2003).

Marchler-Bauer, A. et al. CDD: a conserved domain database for interactive domain family analysis. Nucleic Acids Res. 35 (Database issue): D237–D240 (2007).

Finn, R.D. et al. The Pfam protein families database. Nucleic Acids Res. 36 (Database issue): D281–D288 (2008).

Wass, M.N. & Sternberg, M.J.E. ConFunc—functional annotation in the twilight zone. Bioinformatics 24, 798–806 (2008).

Yao, H. et al. An accurate, sensitive, and scalable method to identify functional sites in protein structures. J. Mol. Biol. 326, 255–261 (2003).

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).

Laskowski, R.A. et al. Protein clefts in molecular recognition and function. Prot. Sci. 5, 2438–2452 (1996).

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).

Jones, D.T. Predicting novel protein folds by using FRAGFOLD. Proteins 45 (Suppl. 5): 127–132 (2001).

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).

Zhang, Y. Template-based modeling and free modeling by I-TASSER in CASP7. Proteins 69 (Suppl. 8): 108–117 (2007).

Hulo, N. et al. The 20 years of PROSITE. Nucleic Acids Res. 36 (Database issue): D245–D249 (2008).