Backbone cluster identification in proteins by a graph theoretical method

Biophysical Chemistry

Volumn 84, Issue 1, 2000, Pages 13-25

  Patra, S M ^a   Vishveshwara, S ^a  

^a INDIAN INSTITUTE OF SCIENCE   (India)

Author keywords

Adjacency matrix; Cluster; Domains; Eigenvalue and eigenvector; Globin family; Non covalent interaction; RNase A family

Indexed keywords

GLOBIN; PROTEIN; RIBONUCLEASE;

ALGORITHM; ARTICLE; CLUSTER ANALYSIS; PRIORITY JOURNAL; PROTEIN FAMILY; PROTEIN FOLDING; PROTEIN STRUCTURE; TECHNIQUE; THEORY;

ALGORITHMS; AMINO ACID SEQUENCE; ANIMALS; APLYSIA; BINDING SITES; CATTLE; CLUSTER ANALYSIS; DATA DISPLAY; GLOBINS; HUMANS; MOLECULAR SEQUENCE DATA; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; RANA PIPIENS; RIBONUCLEASE, PANCREATIC; SEALS, EARLESS; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 0033955344     PISSN: 03014622     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0301-4622(99)00134-9     Document Type: Article

References (30)

1. Baldwin R.L. Nature (London). 346:1990;409-410.
2. Kim P.S., Baldwin R.L. Annu. Rev. Biochem. 59:1990;631-660.
3. Heringa J., Argos P. J. Mol. Biol. 220:1991;151-171.
4. Dill K.A., Bromberg S., Yue K. et al. Protein Sci. 4:1995;561-602.
5. Gromiha M.M., Selvaraj S. Biophys. Chem. 77(1):1999;49-68.
6. Richard F.M. Ann. Rev. Biophys. Bioeng. 6:1977;151-176.
7. Dosztanyi Z., Fiser A., Simon I. J. Mol. Biol. 272:1997;597-611.
8. Sowdhamini R., Blundell T.L. Protein Sci. 4:1995;506-520.
9. Zefus M.H. Protein Sci. 4:1995;1188-1202.
10. Swindells M.B. Protein Sci. 4:1995;93-102.
11. Flower D.R. Protein Eng. 7(11):1994;1305-1310.
12. Koch I., Kaden F., Selbig J. Proteins. 12(4):1992;314-323.
13. Artymiuk P.J., Rice D.W., Mitchell E.M., Willett P. Protein Eng. 4(1):1990;39-43.
14. Haliloglu T., Bahar I., Erman B. Phys. Rev. Lett. 79(16):1997;3090-3093.
15. Bahar I., Atilgan A.R., Jernigan R.L., Erman B. Proteins Struct. Funct. Genet. 29:1997;172-185.
16. Demirel M.C., Atilgan A., Jernigan R.L., Erman B., Bahar I. Protein Sci. 7:1998;2522-2532.
17. Bahar I., Atilgan A.R., Erman B. Fold Des. 2:1997;173-181.
18. Patra S.M., Vishveshwara S. Int. J. Quantum. Chem. 71:1999;349-356.
19. Kannan N., Vishveshwara S. J. Mol. Biol. 292(2):1999;441-464.
20. Encyclopedia of Computational Chemistry, in: P.V.R. Schleyer (Eds.), vol. 2, John Wiley and Sons, NY, Singapore 1998 p. 1174.
21. Panjikar S.K., Biswas M., Vishveshwara S. Acta Crystallogr. D53:1997;627-637.
22. Miyazawa S., Jernigan R.L. Macromolecules. 18:1985;534-552.
23. Miyazawa S., Jernigan R.L. J. Mol. Biol. 256:1996;623-644.
24. Hagen L., Kahng A.B. IEE Trans. Comput. Aided Des. III(9):1992;1074-1084.
25. Gutman I., Cvetkovic D. Croat. Chem. Acta. 49:1977;115-121.
26. Randic M. J. Chem. Inf. Comput. Sci. 15:1975;105.
27. C.M., Cuchillo, M., Vilanova, M.V., Nogues, Ribonucleases Structures and Functions, in: G.D. Alessio, J.F. Riordan (Eds.), copyright by Academic Press 1997, p. 271.
28. Juminaga D., Wedemeyer W.J., Juarez G., McDonald R., Scheraga M.A. H.A. Biochemistry. 36:1997;10131-10145.
29. Lesk A.M., Chothia C.J. Mol. Biol. 136:1980;225-270.
30. Humphrey W., Dalke A., Schulten K. Visual molecular dynamics. J. Mol. Graph. 14(1):1996;33-38.