Cascade PSI-BLAST web server: A remote homology search tool for relating protein domains

Nucleic Acids Research

Volumn 34, Issue WEB. SERV. ISS., 2006, Pages

  Bhadra, R ^a   Sandhya, S ^a,b   Abhinandan, K R ^a,c   Chakrabarti, S ^b,d   Sowdhamini, R ^b   Srinivasan, N ^a  

^a INDIAN INSTITUTE OF SCIENCE   (India)

^b TATA INSTITUTE OF FUNDAMENTAL RESEARCH   (India)

^c UNIVERSITY COLLEGE LONDON   (United Kingdom)

^d NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

ACCESS TO INFORMATION; ARTICLE; COMPUTER PROGRAM; EVOLUTION; INTERMETHOD COMPARISON; INTERNET; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN DOMAIN; PROTEIN FAMILY; PROTEIN FOLDING; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SWISS-PROT; WEB BROWSER; PROTEIN TERTIARY STRUCTURE;

INTERNET; PROTEIN STRUCTURE, TERTIARY; SEQUENCE HOMOLOGY, AMINO ACID; SOFTWARE;

EID: 33747854648     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl157     Document Type: Article

References (13)

1. 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.
2. 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.
3. 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.
4. Sandhya,S., Kishore,S., Sowdhamini,R. and Srinivasan,N. (2003) Effective detection of remote homologues by searching in sequence dataset of a protein domain fold. FEBS Lett., 552, 225-230.
5. Yi,T.M. and Lander,E.S. (1994) Recognition of related proteins by iterative template refinement (ITR). Protein Sci., 3, 1315-1328.
6. Eddy,S.R., Mitchison,G. and Durbin,R. (1995) Maximum discrimination hidden Markov models of sequence consensus. J. Comput. Biol., 2, 9-23.
7. Park,J., Teichmann,S.A., Hubbard,T. and Chothia,C. (1997) Intermediate sequences increase the detection of homology between sequences. J. Mol. Biol., 273, 349-354.
8. Salamov,A.A., Suwa,M., Orengo,C.A. and Swindells,M.B. (1999) Combining sensitive database searches with multiple intermediates to detect distant homologues. Protein Eng., 12, 95-100.
9. Li,W., Pio,F., Pawlowski,K. and Godzik,A. (2000) Saturated BLAST: an automated multiple intermediate sequence search used to detect distant homology. Bioinformatics., 16, 1105-1110.
10. Sandhya,S., Chakrabarti,S., Abhinandan,K.R., Sowdhamini,R. and Srinivasan,N. (2005) Assessment of a rigorous transitive profile based search method to detect remotely similar proteins. J. Biomol. Struct. Dyn., 23, 283-298.
11. Aravind,L. and Koonin,E.V. (1999) Gleaning non-trivial structural, functional and evolutionary information about proteins by iterative database searches. J. Mol. Biol., 287, 1023-1040.
12. Bairoch,A. and Apweiler,R. (2000) The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res., 28, 45-48.
13. Sonnhammer,E.L., Eddy,S.R., Birney,E., Bateman,A. and Durbin,R. (1998) Pfam: multiple sequence alignments and HMM-profiles of protein domains. Nucleic Acids Res., 26, 320-322.