Prediction of ligand binding sites using homologous structures and conservation at CASP8

Proteins: Structure, Function and Bioinformatics

Volumn 77, Issue SUPPL. 9, 2009, Pages 147-151

  Wass, Mark N ^a   Sternberg, Michael J E ^a  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

Author keywords

Binding site; Bioinformatics; CASP; Function prediction; Structural biology

Indexed keywords

PROTEIN; LIGAND;

ACCURACY; ARTICLE; BINDING SITE; COMPUTER MODEL; COMPUTER PREDICTION; LIGAND BINDING; PRIORITY JOURNAL; PROTEIN STRUCTURE; QUALITY CONTROL; AMINO ACID SEQUENCE; BIOLOGY; CHEMISTRY; METHODOLOGY; NUCLEOTIDE SEQUENCE; PROTEIN CONFORMATION; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS;

AMINO ACID SEQUENCE; BINDING SITES; COMPUTATIONAL BIOLOGY; CONSERVED SEQUENCE; LIGANDS; PROTEIN CONFORMATION; PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN;

EID: 74249093489     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22513     Document Type: Article

References (18)

1. Berezin C, Glaser F, Rosenberg J, Paz I, Pupko T, Fariselli P, Casadio R, Ben-Tal N. ConSeq: the identification of functionally and structurally important residues in protein sequences. Bioinformatics 2004; 20: 1322-1324. (Pubitemid 38807587)
2. Lichtarge O, Bourne HR, Cohen FE. An evolutionary trace method defines binding surfaces common to protein families. J Mol Biol 1996; 257: 342-358. (Pubitemid 26114038)
3. Aloy P, Querol E, Aviles FX, Sternberg MJ. Automated structure-based prediction of functional sites in proteins: applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking. J Mol Biol 2001; 311: 395-408. (Pubitemid 32744549)
4. Landau M, Mayrose I, Rosenberg Y, Glaser F, Martz E, Pupko T, Ben-Tal N. ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures. Nucleic Acids Res 2005; 33 (Web Server issue): W299-W302. (Pubitemid 44529930)
5. Glaser F, Morris RJ, Najmanovich RJ, Laskowski RA, Thornton JM. A method for localizing ligand binding pockets in protein structures. Proteins 2006; 62: 479-488. (Pubitemid 43054367)
6. Laskowski RA. SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions. J Mol Graph 1995; 13: 323-330, 307-328.
7. Lopez G, Valencia A, Tress ML. firestar-prediction of functionally important residues using structural templates and alignment reliability. Nucleic Acids Res 2007; 35 (Web Server issue): W573-W577.
8. Brylinski M, Skolnick J. A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation. Proc Natl Acad Sci USA 2008; 105: 129-134.
9. Ginalski K, Elofsson A, Fischer D, Rychlewski L. 3D-Jury: a simple approach to improve protein structure predictions. Bioinformatics 2003; 19: 1015-1018. (Pubitemid 36675823)
10. Russell RB, Sasieni PD, Sternberg MJ. Supersites within superfolds. Binding site similarity in the absence of homology. J Mol Biol 1998; 282: 903-918.
11. Wass MN, Sternberg MJ. ConFunc-functional annotation in the twilight zone. Bioinformatics 2008; 24: 798-806.
12. Finn RD, Mistry J, Schuster-Bockler B, Griffiths-Jones S, Hollich V, Lassmann T, Moxon S, Marshall M, Khanna A, Durbin R, Eddy SR, Sonnhammer EL, Bateman A. Pfam: clans, web tools and services. Nucleic Acids Res 2006; 34 (Database issue): D247-D251.
13. The-Uniprot-Consortium. The Universal Protein Resource (UniProt). Nucleic Acids Res 2007; 35 (Database issue): D193-D197.
14. Porter CT, Bartlett GJ, Thornton JM. The catalytic site atlas: a resource of catalytic sites and residues identified in enzymes using structural data. Nucleic Acids Res 2004; 32 (Database issue): D129-D133.
15. Tress M. CASP8 Function Assessment. Proteins 2009.
16. Matthews BW. Comparison of the predicted and observed secondary structure of T4 phage lysozyme. Biochim Biophys Acta 1975; 405: 442-451.
17. Lopez G, Rojas A, Tress M, Valencia A. Assessment of predictions submitted for the CASP7 function prediction category. Proteins 2007; 69 (Suppl 8): 165-174. (Pubitemid 350210124)
18. LEE. Binding site prediction. Proteins 2009.