Identification of structural domains in proteins by a graph heuristic

Proteins: Structure, Function and Genetics

Volumn 35, Issue 3, 1999, Pages 338-352

  Wernisch, Lorenz ^a   Hunting, Marcel ^b   Wodak, Shoshana J ^a,c  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^b UNIVERSITY OF TWENTE   (Netherlands)

^c UNIVERSITÉ LIBRE DE BRUXELLES   (Belgium)

Author keywords

Branch and bound; Contact area; Protein architecture; Structural motifs; Voronoi polyhedra

Indexed keywords

PROTEIN;

ALGORITHM; ARTICLE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN STRUCTURE; STRUCTURE ANALYSIS;

EVALUATION STUDIES; METHODS; PROTEIN CONFORMATION;

EID: 0033562691     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19990515)35:3<338::AID-PROT8>3.0.CO;2-I     Document Type: Article

References (36)

1. Wetlaufer DB. Nucleation, rapid folding, and globular intrachain regions in proteins. Proc Natl Acad Sci 1973;70:697-701.
2. Go M. Correlation of DNA exonic regions with protein structural units in hemoglobin. Nature 1981;291:90-92.
3. Islam SA, Luo J, Sternberg MJE. Identification and analysis of domains in proteins. Protein Eng 1995;8:513-525.
4. Sowdhamini R, Blundell TL. An automatic method involving cluster analysis of secondary structures for the identification of domains in proteins. Protein Sci 1995;4:506-520.
5. Swindells MB. A procedure for detecting structural domains in proteins. Protein Sci 1995;4:103-112.
6. Rossman M, Rao S. Comparison of supersecondary structures in proteins. J Mol Biol 1973;76:241-256.
7. Rossmann MG, Liljas A. Recognition of structural domains in globular proteins. J Mol Biol 1974;85:177-181.
8. Levitt M, Chothia C. Structural patterns in globular proteins. Nature 1976;261:552.
9. Rose GD. Hierarchic organization of domains in globular proteins. J Mol Biol 1979;134:447-470.
10. Sander C. Physical criteria for folding units of globular proteins. In: Balaban M, editor. Structural aspects of recognition and assembly in biological macromolecules, Vol I: Proteins and protein complexes, fibrous proteins. Jerusalem: Alpha Press; 1981. p 183-195.
11. Janin J, Chothia C. Domains in proteins - definitions, location, and structural principles. Meth Enzymol 1985;115:420-430.
12. Zehfus MH, Rose GD. Compact units in proteins. Biochemistry 1986;25:5759-5756.
13. Kikuchi T, N'emethy G, Scheraga HA. Prediction of the location of structural domains in globular proteins. J Protein Chem 1988;88: 427-471.
14. Holm L, Sander C. Parser for protein folding units. Proteins 1994;19:256-268.
15. Siddiqui AS, Barton GJ. Continuous and discontinuous domains: an algorithm for the automatic generation of reliable protein domain definitions. Protein Sci 1995;4:872-884.
16. Jones S, Stewart M, Michie A, Swindells MB, Orengo C, Thornton JM. Domain assignment for protein structures using a consensus approach: Characterisation and analysis. Protein Sci, 1998;7:233-242.
17. Richardson JS. The anatomy and taxonomy of protein structure. Adv Protein Chem 1981;34:246-253.
18. Wodak J, Janin J. Location of structural domains in proteins. Biochemistry 1981;20:6544-6552. 340 p.
19. Garey MR, Johnson DS. Computers and intractability, a guide to the theory of NP-completeness. San Francisco:W.H. Freeman; 1979. 340 p.
20. Kernighan BW, Lin S. An efficient heuristic procedure for partitioning graphs. Bell Systems Technical J 1970;49:291-307.
21. Nemhauser GL, Wolsey LA. Integer and combinatorial optimization. New York: John Wiley & Sons; 1988. 763 p.
22. Edelsbrunner H. Algorithms in combinatorial geometry. Berlin Heidelberg: Springer; 1987. 423 p.
23. Richards FM. The interpretation of protein structures: total volumes, group volume distributions and packing density. J Mol Biol 1974;82:1-14.
24. Gerstein M, Tsai J, Levitt M. The volumes of atoms on the protein surface calculated from simulations, using Voronoi polyhedra. J Mol Biol 1995; 249:955-966.
25. Harpaz Y, Gerstein M, Chothiai C. Volume changes on protein folding. Structure 1994;2:611-649.
26. Pontius J, Richell J, Wodak SJ. Deviations from standard volumes as a quality measure for protein crystal structures. J Mol Biol 1996;264:121-136.
27. Gellatly BJ, Finney JL. Calculation of protein volumes: an alternative to the Voronoi procedure. J Mol Biol 1982;161:305-322.
28. Rashin AA. Location of domains in globular proteins. Nature 1981;291:85-86.
29. Bernstein F, Koetzle T, Williams G et al. The protein data bank: a computer based archival file for macromolecular structures. J Mol Biol 1977;112:535-542.
30. Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton JM. CATH - A hierarchic classification of protein domain structures. Structure 1997;5:1093-1108.
31. Richards FM. Calculations of molecular volumes and areas for structures of known geometry. Meth Enzymol 1985; 115:440-464.
32. Hunting M. Relaxation techniques for discrete optimization problems. University of Twente, Enschede, Netherlands: Institute for Applied Mathematics; 1998. 150 p.
33. Efron B, Tibshirani R. An introduction to the bootstrap. New York: Chapman and Hall; 1993. 436 p.
34. Colloch N, Etchebest C, Thoreau E, Henrissat B, Mornon JP. Comparison of 3 algorithms for the assignment of secondary structure in proteins - the advantages of a consensus assignment. Protein Eng 1993;6:377-382.
35. Schleinegger MP, Bennet NJ, Eisenberg D,. Oligomer formation by 3D domain swapping: a model for protein assembly and misassembly. Adv Protein Chem 1997;50:61-122.
36. Kraulis PJ. MOLSCRIPT - a program to produce both detailed and schematic plots of protein structures. J Appl Crystallogr 1991:24:946-950.