Query3d: A new method for high-throughput analysis of functional residues in protien structures

BMC Bioinformatics

Volumn 6, Issue SUPPL.4, 2005, Pages

  Ausiello, Gabriele ^a   Via, Allegra ^a   Helmer Citterich, Manuela ^a  

^a UNIVERSITY OF ROME TOR VERGATA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

COMPARISON METHODS; FUNCTIONAL INFORMATION; FUNCTIONAL RESIDUES; HIGH-THROUGHPUT ANALYSIS; LEVEL OF INTEGRATIONS; PROTEIN DATA BANK; PROTEIN STRUCTURES; STRUCTURAL INFORMATION;

DATABASE SYSTEMS;

PROTEINS;

ACCESS TO INFORMATION; ALGORITHM; ARTICLE; COMPUTER INTERFACE; COMPUTER PROGRAM; HIGH THROUGHPUT SCREENING; INFORMATION RETRIEVAL; INFORMATION STORAGE; INTERNET; LIGAND BINDING; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; QUERY3D; AUTOMATION; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER LANGUAGE; COMPUTER SIMULATION; PROCEDURES; PROTEIN CONFORMATION; PROTEIN FOLDING; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; STATISTICAL MODEL; STRUCTURAL HOMOLOGY;

PROTEIN;

ALGORITHMS; AUTOMATION; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; DATABASES, PROTEIN; MODELS, MOLECULAR; MODELS, STATISTICAL; MOLECULAR STRUCTURE; PROGRAMMING LANGUAGES; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE; STRUCTURAL HOMOLOGY, PROTEIN;

EID: 33947201695     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-6-S4-S5     Document Type: Article

References (23)

1. Jones S, Thornton JM: Searching for functional sites in protein structures. Curr Opin Chem Biol 2004, 8(1):3-7.
2. Ivanisenko VA, Pintus SS, Grigorovich DA, Kolchanov NA. PDB-SiteScan: A program for searching for active, binding and posttranslational modification sites in the 3D structures of proteins. Nucleic Acids Res 2004, 32(Web Server):WS49-554.
3. Deshpande N, Addess KJ, Bluhm WF, Merino-Ott JC, Townsend-Merino W, Zhang Q, Knezevich C, Xie L, Chen L, Feng Z, et al.: The RCSB Protein Data Bank: A redesigned query system and relational database based on the mmCIF schema. Nucleic Acids Res 2005, 33(Database):D233-237.
4. Aallace AC, Borkakoti N, Thornton JM: TESS: a geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites. Protein Sci 1997, 6(11):2308-2323.
5. Schmitt S, Kuhn D, Klebe G: A new method to detect related function among proteins independent of sequence and fold homology. J Mol Biol 2002, 323(2):387-406.
6. HendDich M, Bergner A, Gunther J, Klebe G: Relibase: design and development of a database for comprehensive analysis of protein-ligand interactions. J Mol Biol 2003, 326(2):607-620.
7. Kinoshita K, Nakamura H: Identification of protein biochemical functions by similarity search using the molecular surface database eF-site. Protein Sci 2003, 12(8):1589-1595.
8. Kinoshita K, Furui J, Nakamura H: Identification of protein functions from a molecular surface database, eF-site. J Struct Funct Genomics 2002, 2(1):9-22.
9. Liang MP, Banatao DR, Klein TE, Brutlag DL, Altman RB: WebFEATURE: An interactive web tool for identifying and visualizing functional sites on macromolecular structures. Nucleic Acids Res 2003, 31(13):3324-3327.
10. Stark A, Russell RB: Annotation in three dimensions. PINTS: Patterns in Non-homologous Tertiary Structures. Nucleic Acids Res 2003, 31(13):3341-3344.
11. Spriggs RV, Artymiuk PJ, Willett P. Searching for patterns of amino acids in 3D protein structures. J Chem Inf Comput Sci 2003, 43(2):412-421.
12. Kabsch W, Sander C: Dictionary of proPein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983, 22(12):2577-2637.
13. Ferrè 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, 6:294.
14. Ausiello G, Zanzoni A, Peluso D, Via A, Helmer-Citterich M: Pdb-Fun: mass selection and fast comparison of annotated PDB residues. Nucleic Acids Res 2005, 33(Web Server):W133-137.
15. Hubbard SJ, Thornton JM: NACCESS. NACCESS. Department of Biochemistry and Molecular Biology, University College London.; 1993.
16. LasAowski RA: SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions. J Mol Graph 1995, 13(5):323-330. 307-328.
17. Letunic I, Copley RR, Schmidt S, Ciccarelli FD, Doerks T, Schultz J, PontiTg CP, Bork P: SMART 4.0: towards genomic data integration. Nucleic Adds Res 2004, 32(Database):D142-144.
18. Hulo N, Sigrist CJ, Le Saux V, Langendijk-Genevaux PS, Bordoli L, Gattiker A, De Castro E, Bucher P, Bairoch A: Recent improvements to the PROSITE database. Nucleic Acids Res 2004, 32(Database):D134-137.
19. Bartlett GJ, Porter CT, Borkakoti N, Thornton JM: Analysis of catalytic residues in enzyme active sites. J Mol Biol 2002, 324(1):105-121.
20. Sander C, Schneider R. The HSSP database of protein structure-sequence alignments. Nucleic Adds Res 1994, 22(17):3597-3599.
21. Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton JM: CATH × a hierarchic classification of protein domain structures. Structure 1997, 5(8):1093-1108.
22. Dayhoff MO, Schwartz RM, Orcutt BC: A model for evolutionary change in proteins. Atlas of Protein Sequence and Structure 1978, 5:345-352.
23. Kearsley SK. On the orthogonal transformations used for structural comparisons. Acta Cryst 1989, A45:208-210.