DIAL: A web-based server for the automatic identification of structural domains in proteins

Nucleic Acids Research

Volumn 33, Issue SUPPL. 2, 2005, Pages

  Pugalenthi, Ganesan ^b   Archunan, Govindaraju ^a   Sowdhamini, Ramanathan ^b  

^a BHARATHIDASAN UNIVERSITY   (India)

^b TATA INSTITUTE OF FUNDAMENTAL RESEARCH   (India)

Author keywords

[No Author keywords available]

Indexed keywords

ACCESS TO INFORMATION; ARTICLE; AUTOMATION; COMPUTER PROGRAM; CRYSTALLOGRAPHY; EXPERIMENTATION; INTERNET; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN FAMILY; PROTEIN FUNCTION; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; STRUCTURAL GENOMICS; THREE DIMENSIONAL IMAGING; AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; CLIENT SERVER APPLICATION; EXPERIMENTAL DESIGN; STRUCTURE ANALYSIS; CHEMICAL STRUCTURE; CHEMISTRY; PROTEIN MOTIF; PROTEIN TERTIARY STRUCTURE; X RAY CRYSTALLOGRAPHY;

PROTEIN; AMINO ACID;

AMINO ACID MOTIFS; AMINO ACIDS; CRYSTALLOGRAPHY, X-RAY; INTERNET; MODELS, MOLECULAR; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; PROTEINS; SOFTWARE;

EID: 23144453476     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gki427     Document Type: Article

References (31)

1. Ilsley,J.L., Sudol,M. and Winder,S.J. (2002) The WW domain: Linking cell signalling to the membrane cytoskeleton. Cell. Signal., 14, 183-189.
2. Chamnongpol,S. and Li,X. (2004) SH3 domain protein-binding arrays. Methods Mol. Biol., 264, 183-189.
3. Heger,A. and Holm,L. (2003) Exhaustive enumeration of protein domain families. J. Mol. Biol., 328, 749-767.
4. Russell,R.B. (1994) Domain insertion. Protein Eng., 7, 1407-1410.
5. Finn,R.D., Marshall,M. and Bateman,A. (2005) iPfam: Visualization of protein-protein interactions in PDB at domain and amino acid resolutions. Bioinformatics, 21, 410-412.
6. Murzin,A.G., Brenner,S.E., Hubbard,T. and Chothia,C. (1995) SCOP: A structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol., 247, 536-540.
7. Marchler-Bauer,A., Anderson,J.B., Cherukuri,P.F., DeWeese-Scott,C., Geer,L.Y., Gwadz,M., He,S., Hurwitz,D.I., Jackson,J.D., Ke,Z. et al. (2005) CDD: A conserved domain database for protein classification. Nucleic Acids Res., 33, D192-D196.
8. Bateman,A., Coin,L., Durbin,R., Finn,R.D., Hollich,V., Griffiths-Jones,S., Khanna,A., Marshall,M., Moxon,S., Sonnhammer,E.L. et al. (2004) The Pfam protein families database. Nucleic Acids Res., 32, D138-D141.
9. Liu,J. and Rost,B. (2004) CHOP: Parsing proteins into structural domains. Nucleic Acids Res., 32, W569-W571.
10. Dengler,U., Siddiqui,A.S. and Barton,G.J. (2001) Protein structural domains: Analysis of the 3Dee domains database. Proteins, 42, 332-344.
11. Pugalenthi,G., Bhaduri,A. and Sowdhamini,R. (2005) GenDiS: Genomic distribution of protein structural domain superfamilies. Nucleic Acids Res., 33, D252-D255.
12. Alexandrov,N. and Shindyalov,I. (2003) PDP: Protein Domain Parser. Bioinformatics, 19, 429-430.
13. Taylor,W.R. (1999) Protein structural domain identification. Protein Eng., 12, 203-216.
14. Schulz,G.E. (1977) Structural rules for globular proteins. Angew. Chem. Int. Ed. Engl., 16, 23-32.
15. Swindells,M.B. (1995) A procedure for detecting structural domains in proteins. Protein Sci., 4, 103-112.
16. Xu,Y., Xu,D. and Gabow,H.N. (2000) Protein domain decomposition using a graph-theoretic approach. Bioinformatics, 16, 1091-1104.
17. Sowdhamini,R. and Blundell,T.L. (1995) An automatic method involving cluster analysis of secondary structures for the identification of domains in proteins. Protein Sci., 4, 506-520.
18. Siddiqui,A.S., Dengler,U. and Barton,G.J. (2001) 3Dee: A database of protein structural domains. Bioinformatics, 17, 200-201.
19. Vinayagam,A., Shi,J., Pugalenthi,G., Meenakshi,B., Blundell,T.L. and Sowdhamini,R. (2003) DDBASE2.0: Updated domain database with improved identification of structural domains. Bioinformatics, 19, 1760-1764.
20. Orengo,C.A., Michie,A.D., Jones,S., Jones,D.T., Swindells,M.B. and Thornton,J.M. (1997) CATH - a hierarchic classification of protein domain structures. Structure, 5, 1093-1108.
21. Liu,Y. and Eisenberg,D. (2002) 3D domain swapping: As domains continue to swap. Protein Sci., 11, 1285-1299.
22. Sayle,R.A. and Milner-White,E.J. (1995) RASMOL: Biomolecular graphics for all. Trends Biochem. Sci., 20, 374.
23. Kraulis,P.J. (1991) MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr., 24, 946-950.
24. Mizuguchi,K., Deane,C.M., Blundell,T.L., Johnson,M.S. and Overington,J.P. (1998) JOY: Protein sequence-structure representation and analysis. Bioinformatics, 14, 617-623.
25. Altschul,S.F., Madden,T.L., Schaffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
26. Bourne,P.E., Addess,K.J., Bluhm,W.F., Chen,L., Deshpande,N., Feng,Z., Fleri,W., Green,R., Merino-Ott,J.C., Townsend-Merino,W. et al. (2004) The distribution and query systems of the RCSB Protein Data Bank. Nucleic Acids Res., 32, D223-D225.
27. Thompson,J.D., Higgins,D.G. and Gibson,T.J. (1994) CLUSTALW: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
28. Bhaduri,A., Pugalenthi,G., Gupta,N. and Sowdhamini,R. (2004) iMOT: An interactive package for the selection of spatially interacting motifs. Nucleic Acids Res., 32, W602-W605.
29. Sigrist,C.J., Cerutti,L., Hulo,N., Gattiker,A., Falquet,L., Pagni,M., Bairoch,A. and Bucher,P. (2002) PROSITE: A documented database using patterns and profiles as motif descriptors. Brief. Bioinformatics, 3, 265-274.
30. Lee,B. and Richards,F.M. (1971) The interpretation of protein structures: Estimation of static accessibility. J. Mol. Biol., 55, 379-400.
31. Chance,M.R., Fiser,A., Sali,A., Pieper,U., Eswar,N., Xu,G., Fajardo,J.E., Radhakannan,T. and Marinkovic,N. (2004) High-throughput computational and experimental techniques in structural genomics. Genome Res., 14, 2145-2154.