FunClust: A web server for the identification of structural motifs in a set of non-homologous protein structures

BMC Bioinformatics

Volumn 9, Issue SUPPL. 2, 2008, Pages

  Ausiello, Gabriele ^a   Gherardini, Pier Federico ^a   Marcatili, Paolo ^b   Tramontano, Anna ^b   Via, Allegra ^a   Helmer Citterich, Manuela ^a  

^a UNIVERSITY OF ROME TOR VERGATA   (Italy)

^b SAPIENZA UNIVERSITY OF ROME   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

CLUSTERING PROCEDURE; CONSERVED RESIDUES; DIFFERENT STRUCTURE; FUNCTIONAL FEATURES; HOMOLOGOUS PROTEINS; NUCLEOTIDE SEQUENCES; PROTEIN STRUCTURES; STRUCTURAL COMPARISON;

AMINO ACIDS; NUCLEIC ACIDS;

PROTEINS;

FERREDOXIN; LIM PROTEIN; SERINE PROTEINASE; ZINC BINDING PROTEIN; PROTEIN;

ACCESS TO INFORMATION; AMINO ACID SEQUENCE; ARTICLE; CLIENT SERVER APPLICATION; CLUSTER ANALYSIS; COMPUTER GRAPHICS; COMPUTER PROGRAM; GENETIC CONSERVATION; INTERMETHOD COMPARISON; INTERNET; PROTEIN FUNCTION; PROTEIN MOTIF; PROTEIN STRUCTURE; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; STRUCTURE ANALYSIS; AUTOMATED PATTERN RECOGNITION; CHEMISTRY; EVALUATION; METHODOLOGY; MOLECULAR GENETICS; SEQUENCE ANALYSIS; ULTRASTRUCTURE;

AMINO ACID MOTIFS; AMINO ACID SEQUENCE; CLUSTER ANALYSIS; INTERNET; MOLECULAR SEQUENCE DATA; PATTERN RECOGNITION, AUTOMATED; PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; SEQUENCE HOMOLOGY, AMINO ACID; SOFTWARE;

EID: 43349087464     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-9-S2-S2     Document Type: Article

References (24)

1. Sandve GK Drablos F A survey of motif discovery methods in an integrated framework Biol Direct 2006, 1:11 1479319 16600018 10.1186/1745-6150-1-11
2. Marcatili P. Bussotti G. Tramontano A. The movin server for the analysis of protein interaction networks BMC Bioinformatics 2008, 9(Suppl 2):S11
3. Novotny M Madsen D Kleywegt GJ Evaluation of protein fold comparison servers Proteins 2004, 54:260-270 10.1002/prot.10553 14696188
4. Hill AD Reilly PJ Comparing programs for rigid-body multiple structural superposition of proteins Proteins 2006, 64:219-226 10.1002/prot.20975 16568449
5. Shatsky M Shulman-Peleg A Nussinov R Wolfson HJ The multiple common point set problem and its application to molecule binding pattern detection J Comput Biol 2006, 13:407-428 10.1089/cmb.2006.13.407 16597249
6. Shatsky M Nussinov R Wolfson HJ A method for simultaneous alignment of multiple protein structures Proteins 2004, 56:143-156 10.1002/prot.10628 15162494
7. Moodie SL Mitchell JB Thornton JM Protein recognition of adenylate: An example of a fuzzy recognition template J Mol Biol 1996, 263:486-500 10.1006/jmbi.1996.0591 8918603
8. Denessiouk KA Rantanen VV Johnson MS Adenine recognition: A motif present in atp-, coa-, nad-, nadp-, and fad-dependent proteins Proteins 2001, 44:282-291 10.1002/prot.1093 11455601
9. Henschel A Kim WK Schroeder M Equivalent binding sites reveal convergently evolved interaction motifs Bioinformatics 2006, 22:550-555 10.1093/bioinformatics/bti782 16287935
10. The FunClust web server http://pdbfun.uniroma2.it/funclust
11. Ausiello G Via A Helmer-Citterich M Query3d: A new method for high-throughput analysis of functional residues in protein structures BMC Bioinformatics 2005, 6(Suppl 4):S5 10.1186/1471-2105-6-S4-S5 16351754 1866380
12. Wallace AC Laskowski RA Thornton JM Derivation of 3d coordinate templates for searching structural databases: Application to ser-his-asp catalytic triads in the serine proteinases and lipases Protein Sci 1996, 5:1001-1013 2143436 8762132
13. Stark A Sunyaev S Russell RB A model for statistical significance of local similarities in structure J Mol Biol 2003, 326:1307-1316 10.1016/ S0022-2836(03)00045-7 12595245
14. Jones S Thornton JM Searching for functional sites in protein structures Curr Opin Chem Biol 2004, 8:3-7 10.1016/j.cbpa.2003.11.001 15036149
15. Ferre F Ausiello G Zanzoni A Helmer-Citterich M Functional annotation by identification of local surface similarities: A novel tool for structural genomics BMC Bioinformatics 2005, 6:194 1190158 16076399 10.1186/1471-2105-6-194
16. Gherardini PF Wass MN Helmer-Citterich M Sternberg MJE Convergent evolution of enzyme active sites is not a rare phenomenon J Mol Biol 2007, 372:817-845 10.1016/j.jmb.2007.06.017 17681532
17. Berman HM Westbrook J Feng Z Gilliland G Bhat TN Weissig H Shindyalov IN Bourne PE The protein data bank Nucleic Acids Res 2000, 28:235-242 102472 10592235 10.1093/nar/28.1.235
18. Hulo N Bairoch A Bulliard V Cerutti L De Castro E Langendijk-Genevaux PS Pagni M Sigrist CJA The prosite database Nucleic Acids Res 2006, 34:D227-30 1347426 16381852 10.1093/nar/gkj063
19. 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:D129-33 308762 14681376 10.1093/nar/ gkh028
20. Ausiello G Zanzoni A Peluso D Via A Helmer-Citterich M Pdbfun: Mass selection and fast comparison of annotated pdb residues Nucleic Acids Res 2005, 33:W133-7 1160259 15980442 10.1093/nar/gki499
21. Puntervoll P Linding R Gemund C Chabanis-Davidson S Mattingsdal M Cameron S Martin DMA Ausiello G Brannetti B Costantini A Ferre F Maselli V Via A Cesareni G Diella F Superti-Furga G Wyrwicz L Ramu C McGuigan C Gudavalli R Letunic I Bork P Rychlewski L Kuster B Helmer-Citterich M Hunter WN Aasland R Gibson TJ Elm server: A new resource for investigating short functional sites in modular eukaryotic proteins Nucleic Acids Res 2003, 31:3625-3630 168952 12824381 10.1093/nar/gkg545
22. Greene LH Lewis TE Addou S Cuff A Dallman T Dibley M Redfern O Pearl F Nambudiry R Reid A Sillitoe I Yeats C Thornton JM Orengo CA The cath domain structure database: New protocols and classification levels give a more comprehensive resource for exploring evolution Nucleic Acids Res 2007, 35:D291-7 1751535 17135200 10.1093/nar/gkl959
23. Stockwell GR Thornton JM Conformational diversity of ligands bound to proteins J Mol Biol 2006, 356:928-944 10.1016/j.jmb.2005.12.012 16405908
24. Via A Ferre F Brannetti B Valencia A Helmer-Citterich M Three-dimensional view of the surface motif associated with the p-loop structure: Cis and trans cases of convergent evolution J Mol Biol 2000, 303:455-465 10.1006/jmbi.2000.4151 11054283