Identification of domains and domain interface residues in multidomain proteins from graph spectral method

Proteins: Structure, Function and Genetics

Volumn 59, Issue 3, 2005, Pages 616-626

  Sistla, Ramesh K ^a   Brinda, K V ^a   Vishyeshwara, Saraswathi ^a  

^a INDIAN INSTITUTE OF SCIENCE   (India)

Author keywords

Domain interface; Eigen spectra; Protein domain; Protein structure graph; Vector component

Indexed keywords

PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; GRAPH SPECTRAL METHOD; MATHEMATICAL ANALYSIS; METHODOLOGY; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN INTERACTION; PROTEIN STRUCTURE; PROTEIN TERTIARY STRUCTURE; STRUCTURE ANALYSIS;

AMINO ACIDS; BINDING SITES; DATABASES, PROTEIN; PROTEIN CONFORMATION; PROTEINS;

EID: 17844384545     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20444     Document Type: Article

References (17)

1. Richardson JS. The anatomy and taxonomy of protein structure. Adv Protein Chem 1981;34:167-339.
2. Swindells MB. A procedure for the automatic determination of hydrophobic cores in protein structures. Protein Sci 1995;4:93-102.
3. Holm L, Sander C. The FSSP database of structurally aligned protein fold families, Nucl Acid Res 1994;22:3600-3609.
4. Siddiqui AS, Barton GJ. Continous and dicontinous domains: an algorithm for the automatic generation of reliable protein domain definitions. Protein Sci 1995;4:872-884.
5. Islam SA, Luo J, Sternberg MJE. Identification and analysis of domains in proteins. Protein Eng 1995;8:513-525.
6. Sowdhamini R, Rufino SD, Blundell TL. A database of globular protein structural domains: clustering of representative family members into similar folds, Fold Des 1996;1:209-220.
7. Jones S, Stewart M, Michie A, Swindells MB, Orengo C, Thorton JM. Domain assignment for protein structures using a consensus approach: characterization and analysis. Protein Science 1998;7: 233-242.
8. Conte LL, Ailey B, Hubbard TJP, Brenner SE, Murzin AG, Chothia C. SCOP: a structural classification of protein database. Nucleic Acid Res 2000;28:257-259.
9. Veretnik S, Bourne PE, Alexandrov NN, Shindyalov IN. Toward consistent assignment of structural domains in proteins. J Mol Biol 2004;339:647-678.
10. Y. Xu, D. Xu, Gabow HN. Protein domain decomposition using a graph-theoretic approach. Bioinformatics 2000;16:1091-1104.
11. 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.
12. Patra S, Vishveshwara S. Backbone cluster identification in proteins by a graph theoretical method. Biophys Chem 2000;84:13-25.
13. Kannan N, Vishveshwara S. Identification of side-chain clusters in protein structures by a graph spectral method. J Mol Biol 1999;292:441-464.
14. Hall KM. An r-dimensional quadratic placement algorithm. Manage Sci 1970;17:219-229.
15. nd Ed., New York, San Francisco: Freeman; 1996.
16. Humphrey W, Dalke A, Schulten K. VMD-Visual Molecular Dynamics. J Mol Graph 1996;14:33-38.
17. Jones S, Marin A, Thornton JM. Protein domain interfaces: characterization and comparison with oligomeric protein interfaces. Protein Eng 2000;13:77-82.