Predicting metal-binding site residues in low-resolution structural models

Journal of Molecular Biology

Volumn 342, Issue 1, 2004, Pages 307-320

  Sodhi, Jaspreet Singh ^a   Bryson, Kevin ^a   McGuffin, Liam J ^a   Ward, Jonathan J ^a   Wernisch, Lorenz ^b   Jones, David T ^a  

^a UNIVERSITY COLLEGE LONDON   (United Kingdom)

^b UNIVERSITY OF LONDON   (United Kingdom)

Author keywords

functional site; metal binding; model proteins; PSSM; structural genomics

Indexed keywords

ACCURACY; ARTICLE; DATA BASE; FEASIBILITY STUDY; GENE SEQUENCE; GENOME; GENOMICS; HAEMOPHILUS INFLUENZAE TYPE A; INFORMATION; METAL BINDING; NERVE CELL NETWORK; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN MOTIF; PROTEIN STRUCTURE; STRUCTURE ANALYSIS;

HAEMOPHILUS; HAEMOPHILUS INFLUENZAE;

EID: 4143055915     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2004.07.019     Document Type: Article

References (33)

1. H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, and H. Weissig The Protein Data Bank Nucl. Acids Res. 28 2000 235 242
2. C.A. Orengo, A.D. Michie, S. Jones, D.T. Jones, M.B. Swindells, and J.M. Thornton CATH: a hierarchic classification of protein domain structure Structure 5 1997 1093 1108
3. A.G. Murzin, S.E. Brenner, T. Hubbard, and C. Chothia SCOP: a structural classification of proteins database for the investigation of sequences and structures J. Mol. Biol. 247 1995 536 540
4. L. Holm, and C. Sander Mapping the protein universe Science 273 1996 595 602
5. P.J. Artymiuk, A. Poirrette, H.M. Grindley, D.W. Rice, and P. Willett A graph-theoretic approach to the identification of three-dimensional pattern of amino acid side-chains in protein structures J. Mol. Biol. 243 1994 327 344
6. A.C. Wallace, N. Borkakoti, and J.M. Thornton TESS: a geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites Protein Sci. 6 1996 2308 2323
7. 1 ribonucleases J. Mol. Biol. 281 1998 949 968
8. G.T. Kleywegt Recognition of spatial motifs in protein structures J. Mol. Biol. 285 1999 1887 1897
9. C.B. Bagley, and R.B. Altman Characterizing the microenviroment surrounding protein site Protein Sci. 4 1995 622 935
10. L. Wei, E.S. Huang, and R.B. Altman Are predicted structures good enough to preserve functional sites? Struct. Fold. Des. 7 1999 643 650
11. S.F. Altschul, T.L. Madden, A.A. Schäffer, J. Zhang, Z. Zhang, W. Miller, and D.J. Lipman Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucl. Acids Res. 25 1997 3389 3402
12. K. Hofmann, P. Bucher, L. Falquet, and A. Bairoch The Prosite Database, its status in 1999 Nucl. Acids Res. 27 1999 215 219
13. T.K. Attwood, M.D. Croning, D.R. Flower, A.P. Lewis, J.E. Mabey, and P. Scordis PRINTS-S: the database formerly known as PRINTS Nucl. Acids Res. 28 2000 225 227
14. A. Bateman, E. Birney, R. Durbin, S.R. Eddy, K.L. Howe, and E. Sonnhammer The Pfam protein families database Nucl. Acids Res. 28 2000 263 266
15. J.G. Henikoff, E.A. Greene, S. Pietrokovoski, and S. Henikoff Increased coverage of protein families with the Blocks database servers Nucl. Acids Res. 28 2000 228 230
16. R. Apweiler, T. Attwood, A. Bairoch, A. Bateman, E. Birney, and M. Biswas The InterPro database, an integrated documentation resource for protein families, domains and functional sites Nucl. Acids Res. 29 2001 37 40
17. M. Rinaldis, G. Ausiello, G. Cesareni, and M. Helmer-Citterich Three-dimensional profiles: a new tool of identify protein surface similarities J. Mol. Biol. 284 1998 1211 1221
18. A. Via, F. Ferre, B. Brannetti, A. Valencia, and M. Helmer-Citterich Three-dimensional view of the surface motif associated with the P-loop structure: cis and trans cases of convergent evolution J. Mol. Biol. 303 2000 1211 1221
19. S. Karlin, Z.Y. Zhu, and K.D. Karlin The extended environment of mononuclear metal centers in protein structures Proc. Natl Acad. Sci. USA 94 1997 14225 14230
20. D.S. Gregory, C.R. Martin, J.C. Cheetham, and R.A. Rees The prediction and characterization of metal binding sites in proteins Protein Eng. 6 1993 29 35
21. L. Rychlewski, D. Fischer, and A. Elofsson LiveBench-6: large-scale automated evaluation of protein structure prediction servers Proteins: Struct. Funct. Genet. Supplement 53 2003 542 547
22. S. Thore, F. Mauxion, B. Seraphin, and D. Suck X-ray structure and activity of the yeast Pop2 protein: a nuclease subunit of the mRNA deadenylase complex EMBO Rep. 12 2003 1150 1155
23. D.T. Jones GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences J. Mol. Biol. 287 1999 797 815
24. L.J. McGuffin, and D.T. Jones Improvement of the GenTHREADER method for genomic fold recognition Bioinformatics 19 2003 874 881
25. L.J. McGuffin, S. Street, S. Sorensen, and D.T. Jones The genomic threading database Bioinformatics 20 2004 131 132
26. L.J. McGuffin, S. Street, K. Bryson, S. Sorensen, and D.T. Jones The Genomic Threading Database: a comprehensive resource for structural annotations of the genomes from key organisms Nucl. Acids Res. 32 2004 D196 D199
27. D.T. Jones Protein secondary structure prediction based on position-specific scoring matrices J. Mol. Biol. 292 1999 195 202
28. N. Siew, A. Elofsson, L. Rychlewski, and D. Fischer MaxSub: an automated measure for the assessment of protein structure prediction quality Bioinformatics 16 2000 776 785
29. J. Wang, B.D. Sykes, and R. Ryan Structural basis for the conformational adaptability of apolipophorin III, a helix-bundle exchangeable apolipoprotein Proc. Natl Acad. Sci. USA 99 2002 1188 1193
30. W. Kabsch, and C. Sander Dictionary of protein secondary structure. Pattern recognition and hydrogen-bonded and geometrical features Biopolymers 22 1983 2277 2637
31. Riedmiller, M. & Heinrich, B. (1993). A direct adaptive method for faster backpropagation learning: the Rprop algorithm. Proceedings of the ICNN.
32. R. Ihaka, and R. Gentleman R: a language for data analysis and graphics J. Comput. Graph. Stat. 5 1996 299 314
33. W. Humphrey, A. Dalke, and K. Schulten VMD - visual molecular dynamic J. Mol. Graph. 14 1996 33 38