A novel method for comparing topological models of protein structures enhanced with ligand information

Bioinformatics

Volumn 24, Issue 23, 2008, Pages 2698-2705

  Veeramalai, Mallika ^a,b   Gilbert, David ^a,c  

^a UNIVERSITY OF GLASGOW   (United Kingdom)

^b BURNHAM INSTITUTE   (United States)

^c BRUNEL UNIVERSITY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

LIGAND;

ACCURACY; ARTICLE; BIOCHEMICAL COMPOSITION; COMPARATIVE STUDY; COMPUTER PROGRAM; INTERMETHOD COMPARISON; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN LOCALIZATION; PROTEIN PROTEIN INTERACTION; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; STRUCTURE ANALYSIS;

ALGORITHMS; ANIMALS; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; HUMANS; LIGANDS; PROTEIN CONFORMATION; PROTEINS;

EID: 56649091418     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btn518     Document Type: Article

References (39)

1. Altschul,S.F. et al. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402.
2. Barton,G.J. (1996) Protein sequence alignment and database searching. In Sternberg,M.J.E. (ed.) Protein Structure Prediction - A practical approach. Oxford University Press, pp. 31-64.
3. Barton,G.J. (1997) OC - a cluster analysis program. University of Dundee, Scotland, UK. Available at www.compbio.dundee.ac.uk/downloads/oc.
4. Berman,H.M. et al. (2002) The Protein Data Bank. Acta Crystallogr. D Biol. Crystallogr., 58, 899-907.
5. Berman,H.M. et al. (2000) The Protein Data Bank and the challenge of structural genomics. Nat. Struct. Biol., 7 (Suppl. 1), 957-959.
6. Bourne,P. et al. (1997) The macromolecular Crystallographic Information File (mmCIF). Meth. Enzymol., 277, 571-590.
7. Bradley,A.P. (1997) The use of the area under the ROC curve in the evaluation of machine learning algorithms. Pattern Recognit., 30, 1145-1159.
8. Bray,J.E. et al. (2000) The CATH Dictionary of Homologous Superfamilies (DHS): A consensus approach for identifying distant structural homologues. Protein Eng., 13, 153-165.
9. Brazma,A. et al. (1998) Approaches to the automatic discovery of patterns in biosequences. J. Comput. Biol., 5, 279-305.
10. Brenner,S.E. et al. (2000) The ASTRAL compendium for protein structure and sequence analysis. Nucleic Acids Res., 28, 254-256.
11. Chalk,A.J. et al. (2004) PDBLIG: Classification of small molecular protein binding in the Protein Data Bank. J. Med. Chem., 47, 3807-3816.
12. Chandonia,J.M. et al. (2004) The ASTRAL Compendium in 2004. Nucleic Acids Res., 32, D189-D192.
13. Doolittle,R.F. (1995) The multiplicity of domains in proteins. Annu. Rev. Biochem., 64, 287-314.
14. Gilbert,D. et al. (1999) Motif-based searching in TOPS protein topology databases. Bioinformatics, 15, 317-326.
15. Gilbert,D. et al. (2000) Topology-based protein structure comparison using a pattern discovery technique. In Martin,A. and Corne,D. (eds) Proceedings of the AISB-00 Symposium on AI in Bioinformatics. The Society for the Study of Artificial Intelligence and the Simulation of Behaviour, pp. 11-17.
16. Gilbert,D. et al. (2001) A computer system to perform structure comparison using TOPS representations of protein structure. Comput. Chem., 26, 2-0.
17. Gromiha,M.M. et al. (2004) Locating the stabilizing residues in (alpha/beta)8 barrel proteins based on hydrophobicity, long-range interactions, and sequence conservation. Proteins, 55, 316-329.
18. Harrison,A. et al. (2003) Recognizing the fold of a protein structure. Bioinformatics, 19, 1748-1759.
19. Higgins,D.G. (1994) CLUSTAL V: Multiple alignment of DNA and protein sequences. Methods Mol. Biol., 25, 307-318.
20. Holm,L. and Park,J. (2000) DaliLite workbench for protein structure comparison. Bioinformaitcs, 16, 566-567.
21. Koch,I. et al. (1996) An algorithm for finding maximal common subtopologies in a set of protein structures. J. Comput. Biol., 3, 289-306.
22. Madej,T. et al. (1995) Threading a database of protein cores. Proteins, 23, 356-369.
23. Mallika,V. et al. (2002) PASS2: A semi-automated database of protein alignments organised as structural superfamilies. Nucleic Acids Res., 30, 284-288.
24. Michalopoulos,I. et al. (2004) TOPS: An enhanced database of protein structural topology. Nucleic Acids Res., 32 (Database issue), D251-D254.
25. Mizuguchi,K. and Blundell,T. (2000) Analysis of conservation and substitutions of secondary structure elements within protein superfamilies. Bioinformatics, 16, 1111-1119.
26. Nagano,N. et al. (2002) One fold with many functions: The evolutionary relationships between TIM barrel families based on their sequences, structures and functions. J.Mol. Biol., 321, 741-765.
27. Nobeli,I. et al. (2005) A ligand-centric analysis of the diversity and evolution of protein ligand relationships in E.coli. J. Mol. Biol., 347, 415-436.
28. Orengo,C.A. and Taylor,W.R. (1996) SSAP: Sequential structure alignment program for protein structure comparison. Methods Enzymol., 266 617-635.
29. Russell,R.B. and Barton,G.J. (1994) Structural features can be unconserved in proteins with similar folds. An analysis of side-chain to side-chain contacts secondary structure and accessibility. J. Mol. Biol., 244, 332-350.
30. Sowdhamini,R. et al. (1998) CAMPASS: A database of structurally aligned protein superfamilies. Structure, 6, 1087-1094.
31. Sternberg,M.J.E. and Thornton,J.M. (1977) On the conformation of proteins: The handedness of the connection between parallel beta-strans. J. Mol. Biol., 110, 269-283.
32. Torrance,G.M. et al. (2005) Protein structure topological comparison, discovery and matching service. Bioinformatics, 21 2537-2538.
33. Veeramalai,M. et al. (2008) TOPS++FATCAT: Fast flexible structural alignment using constraints derived from TOPS+ strings model. BMC Bioinformatics, 9, 358.
34. Viksna,J. and Gilbert,D. (2001) Pattern matching and pattern discovery algorithms for protein topologies. In 1st International Workshops on Algorithms in Bioinformatics, Vol. 2149 of LNCS. Springer-Verlag, Berlin/Heidelberg, pp. 98-111.
35. von Grotthuss,M. et al. (2003) Ligand Info, searching for similar small compounds using index profiles. Bioinformatics, 19, 1041-1042.
36. Westhead,D.R. et al. (1998) An atlas of protein topology cartoons available on the World Wide Web. Trends Biochem. Sci., 23, 35-36.
37. Westhead,D.R. et al. (1999) Protein structural topology: Automated analysis, diagrammatic representation and database searching. Protein Sci., 8, 897-904.
38. Xue,L. et al. (1999) Database searching for compounds with similar biological activity using short binary bit string representations of molecules. J. Chem. Inf. Comput. Sci., 39, 881-886.
39. Ye,Y. and Godzik,A. (2003) Flexible structure alignment by chaining aligned fragment pairs allowing twists. Bioinformatics, 19 (Suppl. 2), II246-II255.