Structure-based de novo prediction of zinc-binding sites in proteins of unknown function

Bioinformatics

Volumn 27, Issue 9, 2011, Pages 1262-1268

  Zhao, Wei ^a,b   Xu, Meng ^a,b   Liang, Zhi ^a,b   Ding, Bo ^a,b   Niu, Liwen ^a,b   Liu, Haiyan ^a,b   Teng, Maikun ^a,b  

^a UNIVERSITY OF SCIENCE AND TECHNOLOGY OF CHINA   (China)

^b INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

Author keywords

[No Author keywords available]

Indexed keywords

LIGAND; PROTEIN; ZINC;

ARTICLE; BINDING SITE; CHEMISTRY; METABOLISM; PROTEIN BINDING; PROTEIN TERTIARY STRUCTURE; SENSITIVITY AND SPECIFICITY;

BINDING SITES; LIGANDS; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; PROTEINS; SENSITIVITY AND SPECIFICITY; ZINC;

EID: 79954524893     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btr133     Document Type: Article

References (24)

1. Andreini,C. et al. (2004) A hint to search for metalloproteins in gene banks. Bioinformatics, 20, 1373-1380.
2. Andreini,C. et al. (2006) Counting the zinc-proteins encoded in the human genome. J. Proteome Res., 5, 196-201.
3. Andreini,C. et al. (2009) Metalloproteomes: a bioinformatic approach. Acc. Chem. Res., 42, 1471-1479.
4. Babor,M. et al. (2008) Prediction of transition metal-binding sites from apo protein structures. Proteins, 70, 208-217.
5. Bernstein,F.C. et al. (1977) The Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol., 112, 535-542.
6. Bertini,I. et al. (2010) The annotation of full zinc proteomes. J. Biol. Inorg. Chem., 15, 1071-1078.
7. Bordner,A.J. (2008) Predicting small ligand binding sites in proteins using backbone structure. Bioinformatics, 24, 2865-2871.
8. DeLano,W.L. (2002) The PyMOL Molecular Graphics System. DeLano Scientific, San Carlos, CA, USA.
9. Ebert,J.C. and Altman,R.B. (2008) Robust recognition of zinc binding sites in proteins. Protein Sci., 17, 54-65.
10. Gomis-Ruth,F.X. (2003) Structural aspects of the metzincin clan of metalloendopeptidases. Mol. Biotechnol., 24, 157-202.
11. Goyal,K. and Mande,S.C. (2008) Exploiting 3D structural templates for detection of metal-binding sites in protein structures. Proteins, 70, 1206-1218.
12. Holm,R.H. et al. (1996) Structural and functional aspects of metal sites in biology. Chem. Rev., 96, 2239-2314.
13. Janowski,R. et al. (2008) Bacterioferritin from Mycobacterium smegmatis contains zinc in its di-nuclear site. Protein Sci., 17, 1138-1150.
14. Levy,R. et al. (2009) Prediction of 3D metal binding sites from translated gene sequences based on remote-homology templates. Proteins, 76, 365-374.
15. Lin,C.T. et al. (2005) Protein metal binding residue prediction based on neural networks. Int. J. Neural Syst., 15, 71-84.
16. Lin,H.H. et al. (2006) Prediction of the functional class of metal-binding proteins from sequence derived physicochemical properties by support vector machine approach. BMC Bioinformatics, 7 (Suppl. 5), S13.
17. Lin,L. et al. (2007) Crystal structure of Pyrococcus horikoshii PPC protein at 1.60 A resolution. Proteins, 67, 505-507.
18. Lippi,M. et al. (2008) MetalDetector: a web server for predicting metal-binding sites and disulfide bridges in proteins from sequence. Bioinformatics, 24, 2094-2095.
19. Matthews,J.M. et al. (2008) Designed metal-binding sites in biomolecular and bioinorganic interactions. Curr. Opin. Struct. Biol., 18, 484-490.
20. Passerini,A. et al. (2006) Identifying cysteines and histidines in transition-metal-binding sites using support vector machines and neural networks. Proteins, 65, 305-316.
21. Passerini,A. et al. (2007) Predicting zinc binding at the proteome level. BMC Bioinformatics, 8, 39-51.
22. Schymkowitz,J.W.H. et al. (2005) Prediction of water and metal binding sites and their affinities by using the Fold-X force field. Proc. Natl Acad. Sci. USA, 102, 10147-10152.
23. Shu,N. et al. (2008) Prediction of zinc-binding sites in proteins from sequence. Bioinformatics, 24, 775-782.
24. Sodhi,J.S. et al. (2004) Predicting metal-binding site residues in low-resolution structural models. J. Mol. Biol., 342, 307-320.