A graph spectral analysis of the structural similarity network of protein chains

Proteins: Structure, Function and Genetics

Volumn 61, Issue 1, 2005, Pages 152-163

  Krishnadev, O ^a   Brinda, K V ^a   Vishveshwara, Saraswathi ^a  

^a INDIAN INSTITUTE OF SCIENCE   (India)

Author keywords

Eigenvalue and eigenvector components of graphs; Protein chain universe graph; Real world networks; Sub graph density; Weighted graphs

Indexed keywords

FLAVODOXIN; GLUCOSE 6 PHOSPHATE ISOMERASE; HYDROLASE; PLECKSTRIN; PROTEIN;

ARTICLE; PRIORITY JOURNAL; PROTEIN DATA BANK; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; SEQUENCE HOMOLOGY; SIGNAL TRANSDUCTION;

CLUSTER ANALYSIS; DATABASES, PROTEIN; MODELS, MOLECULAR; PROTEIN BINDING; PROTEIN FOLDING; PROTEIN STRUCTURE, QUATERNARY; PROTEINS; STRUCTURAL HOMOLOGY, PROTEIN;

EID: 24344474827     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20532     Document Type: Article

References (22)

1. Wuchty S, Ravasz E, Barabási AL. The architecture of biological networks. In: Deisboeck TS, Yasha Kresh J, Kepler TB, editors. Complex systems in biomedicine. New York: Kluwer Academic Publishing; 2003.
2. Barabási AL. Linked: the new science of networks. Cambridge, MA: Persues Publishing; 2002.
3. Jeong H, Tombor B, Albert R, Oltvai ZN, Barabási AL. The large-scale organization of metabolic networks. Nature 2000;407: 651-654.
4. Farkas I, Jeong H, Vicsek T, Barabási AL, Oltvai ZN. The topology of transcription regulatory network in the yeast, Saccharomyces cerevisiae. Physica A 2003;318:601-612.
5. Yook SY, Oltvai ZN, Barabási AL. Functional and topological characterization of protein interaction networks. Proteomics 2004; 4:928-942.
6. Dokholyan NV, Shakhnovich B, Shakhnovich EI. Expanding protein universe and its origin from the biological Big Bang. Proc Natl Acad Sci USA 2002;9922:14132-14136.
7. Wuchty S. Scale-free behavior in protein domain networks. Mol Biol Evol 2001;18:1694-1702.
8. Kannan N, Vishveshwara S. Identification of side-chain clusters in protein structures by a graph spectral method. J Mol Biol 1999;2922:441-464.
9. Vishveshwara S, Blinda KV, Kannan N. Protein structure: insights from graph theory. J Theor Comput Chem 2002;1:187-211.
10. Sistla RK, Brinda KV, Vishveshwara S. Identification of domains and domain interface residues in multi-domain proteins from graph spectral method. Proteins 2005;59:616-626.
11. Apic G, Gough J, Teichmann SA. Domain combinations in Archeal, Eubacterial, and Eukaryotic proteomes. J Mol Biol 2001;310:311-325.
12. Holm L, Sander C. Protein structure comparison by alignment of distance matrices. J Mol Biol 1993;233:123-138.
13. Holm L, Sander C. Touring protein fold space with DALI/FSSP. Nucleic Acid Res 1998;26:316-319.
14. 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.
15. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997;25: 3389-3402.
16. West DB. Introduction to graph theory. Prentice-Hall of India Private Limited; 2000.
17. Gansner ER, North SC. An open graph visualization system and its applications to software engineering. Softw Pract Exper 1999; 00S1:1-5.
18. Lo Conte L, Brenner SE, Hubbard TJ, Chothia C, Murzin AG. SCOP database in 2002: refinements accommodate structural genomics. Nucleic Acids Res 2002;30:264-267.
19. Deeds EJ, Dokholyan NV, Shakhnovich EI. Protein evolution within a structural space. Biophys J. 2003;855:2962-2972.
20. Koonin EV, Wolf YI, Karev GP. The structure of the protein universe and genome evolution. Nature 2002;420:218-223.
21. Dietmann S, Park J, Notredame C, Heger A, Lappe M, Holm L. A fully automatic evolutionary classification of protein folds: Dali Domain Dictionary version 3. Nucleic Acids Res. 2001;29:55-57.
22. The Gene Ontology Consortium. Gene Ontology: tool for the unification of biology. Nature Genet 2000;25:25-29.