STRALCP - Structure alignment-based clustering of proteins

Nucleic Acids Research

Volumn 35, Issue 22, 2007, Pages

  Zemla, Adam ^a   Geisbrecht, Brian ^b   Smith, Jason ^a   Lam, Marisa ^a   Kirkpatrick, Bonnie ^a   Wagner, Mark ^a   Slezak, Tom ^a   Zhou, Carol Ecale ^a  

^a LAWRENCE LIVERMORE NATIONAL LABORATORY   (United States)

^b UNIVERSITY OF MISSOURI KANSAS CITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; AUTOMATION; CONSERVATION GENETICS; CONTROLLED STUDY; GENE CLUSTER; GENE STRUCTURE; GENETIC ALGORITHM; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN STRUCTURE; SEQUENCE ALIGNMENT; STRUCTURAL BIOINFORMATICS; ALGORITHM; AMINO ACID SEQUENCE; CHEMICAL STRUCTURE; CLASSIFICATION; CLUSTER ANALYSIS; COMPUTER PROGRAM; EVALUATION; INTERNET; MOLECULAR GENETICS; PROTEIN TERTIARY STRUCTURE; STRUCTURAL HOMOLOGY;

PROTEIN;

ALGORITHMS; AMINO ACID SEQUENCE; CLUSTER ANALYSIS; INTERNET; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN STRUCTURE, TERTIARY; PROTEINS; SEQUENCE ALIGNMENT; SOFTWARE; STRUCTURAL HOMOLOGY, PROTEIN;

EID: 38049001118     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkm1049     Document Type: Article

References (24)

1. Dietmann,S. and Holm,L. (2001) Identification of homology in protein structure classification. Nat. Struct. Biol., 8, 953.
2. Redfern,O., Grant,A., Maibaum,M. and Orengo,C. (2005) Survey of current protein family databases and their application in comparative, structural and functional genomics. J. Chromatogr. B, 815, 97-107.
3. Berman,H.M., Westbrook,J., Feng,Z., Gilliland,G., Bhat,T.N., Weissig,H., Shindyalov,I.N. and Bourne,P.E. (2000) The protein data bank. Nucleic Acids Res., 8, 235-242.
4. 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.
5. 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.
6. Holm,L. and Sander,C. (1993) Protein structure comparison by alignment of distance matrices. J. Mol. Biol., 233, 123-138.
7. Holm,L. and Sander,C. (1996) Mapping the protein universe. Science 273, 595-603.
8. Shindyalov,I.N. and Bourne,P.E. (1998) Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng., 11, 739-747.
9. Domingues,F.S., Rahnenfuhrer,J. and Lengauer,T. (2004) Automated clustering of ensembles of alternative models in protein structure databases. Protein Eng., 17, 537-543.
10. Rogen,P. and Fain,B. (2003) Automatic classification of protein structure by using Gauss integrals. Proc. Natl Acad. Sci.USA, 100, 119-124.
11. Aung,Z. and Tan,K.L. (2005) Automatic 3D protein structure classification without structural alignment. J. Comp. Biol., 12 1221-1241.
12. Frishman,D. and Argos,P. (1995) Knowledge-based secondary structure assignment. Proteins Struct. Funct. Genet., 23, 566-579.
13. Cheek,S., Qi,Y., Krishna,S., Kinch,L. and Grishin,N. (2004) SCOPmap: automated assignment of protein structures to evolutionary superfamilies. BMC Bioinformatics, 5, 197.
14. Altschul,S.F., Madden,T.L., Scaffer,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.
15. Ortiz,A.R., Strauss,C.E. and Olmea,O. (2002) MAMMOTH (matching molecular models obtained from theory): An automated method for model comparison. Protein Sci., 11, 2606-2621.
16. Huan,J., Wang,W., Washington,A., Prins,J., Shah,R. and Tropsha,A. (2004) Accurate classification of protein structural families using coherent subgraph analysis. Pacific Symp. Biocomput.; 9, 411-422.
17. Zemla,A. (2003) LGA - a method for finding 3D similarities in protein structures. Nucleic Acids Res., 31, 3370-3374.
18. Geisbrecbt,B.V., Hamaoka,B.Y., Perman,B., Zemla,A. and Leahy,D.J. (2005) The crystal structures of EAP domains from Staphylocaccus aureus reveal an unexpected homology to bacterial superantigens. J. Biol. Chem., 280, 17243-17250.
19. Zemla,A., Ecale Zhou,C., Slezak,T., Kuczmarski,T., Rama, D. Torres,C., Sawicka,D. and Barsky,D. (2005) AS2TS system for protein structure modeling and analysis. Nucleic Acids Res., 33, W111-W115.
20. Hakansson,M., Petersson,K., Nilsson,H., Forsberg,G., Bjork,P., Antonsson,P. and Svensson,L.A. (2000) The crystal structure of staphylococcal enterotoxin H: Implications for binding properties to MHC class II and TcR molerules. J. Mol. Biol., 302, 527-537.
21. Al-Shangiti,A., Naylor,C., Nair,S., Briggs,D., Henderson,B. and Chain,B. (2004) Structural relationships and cellular tropism of staphylococcal superantigen-like proteins. Infect. Immun., 72, 4261-4270.
22. Arcus,V.L., Langley,R., Proft,T., Fraser,J.D. and Baker,E.N. (2002) The three-dimensional structure of a superantigen-like protein, SET3, from a pathogenicity island of the Staphylococcus aureus genome. J. Biol. Chem., 277, 32274-32281.
23. Earhart,C.A., Mitchell,D.T., Murray,D.L., Pinheiro,D.M., Matsumura,M., Schlievert,P.M. and Ohlendorf,D.H. (1998) Structures of five mutants of toxic shock syndrome toxin-1 with reduced biological activity. Biochemistry, 37, 7194-7202.
24. Prasad,G.S., Radhakrishnan,R., Mitchell,D.T., Earhart,C.A., Dinges,M.M., Cook,W.J., Schlievert,P.M. and Ohlendorf,D.H. (1997) Refined structures of three crystal forms of toxic shock syndrome toxin-1 and of a tetramutant with reduced activity. Protein Sci., 6, 1220-1227.