A rapid method for exploring the protein structure universe

Proteins: Structure, Function and Genetics

Volumn 34, Issue 3, 1999, Pages 317-332

  Young, Malin M ^a   Skillman, A Geoffrey ^a   Kuntz, Irwin D ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Fold space; Principal component analysis; Protein family; Protein fingerprinting; Structural comparison

Indexed keywords

ADENOSINE TRIPHOSPHATASE; GLOBIN; HEXOKINASE; IMMUNOGLOBULIN; PROTEIN; SERINE PROTEINASE;

ARTICLE; PRINCIPAL COMPONENT ANALYSIS; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; SEQUENCE HOMOLOGY;

ALGORITHMS; AZURIN; DATABASES, FACTUAL; HEXOKINASE; IMMUNOGLOBULINS; METHODS; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; SERINE ENDOPEPTIDASES;

MAMMALIA;

EID: 0033557364     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19990215)34:3<317::AID-PROT5>3.0.CO;2-7     Document Type: Article

References (39)

1. Chothia C, Lesk A.M. The relation between the divergence of sequence and structure in proteins. Embo J 1986;5:823-826.
2. Allen FH, Bergerhoff G, Sievers R. Protein data bank. In: Crystallographic databases: information content, software systems, scientific applications. Bonn: Data Commission of the International Union of Crystallography. 1987:107-132.
3. Bernstein FC, Koetzle TF, Williams GJB, Meyer EF, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M. The protein data bank: a computer-based archive file for macromolecular structures. J Mol Biol 1977;535-542.
4. Remington SJ, Matthews BW. A systematic approach to the comparison 112:535-542, of protein structures. J Mol Biol 1980; 140:77-199.
5. Taylor WR, Orengo, CA. Protein structure alignment. J Mol Biol 1989;208:1-22.
6. Sali A, Blundell TL. Definition of general topological equivalence in protein structures: a procedure involving comparison of properties and relationships through simulated annealing and dynamic programming. J Mol Biol 1990;212:403-428.
7. Holm L, Sander C. Protein structure comparison by alignment of distance matrices. J Mol Biol 1993;233:123-138.
8. Yee DP, Dill KA. Families and the structural relatedness among globular proteins. Prot Sci 1993;2:884-899.
9. Alexandrov NN, Go N. Common spatial arrangements of backbone fragments in homologous and non-homologous proteins. J Mol Biol 1992;225:5-9.
10. Vriend G. Sander C. Detection of common three-dimensional substructures in proteins. Proteins 1991;11:52-58.
11. Fischer D, Bachar O, Nussinov R, Wolfson H. An efficient automated computer vision based technique for detection of 3-dimensional structural motifs in proteins. J Biomol Struct Dyn 1992;9:769-789.
12. Mitchell EM, Artymuik PJ, Rice DW, Willett P. Use of techniques derived from graph theory to compare secondary structure motifs in proteins. J Mol Biol 1989;212:151-166.
13. Grindley HM, Artymiuk PJ, Rice DW, Willett P. Identification of tertiary structure resemblance in proteins using a maximal common subgraph isomorphism algorithm. J Mol Biol 1993;229: 707-721.
14. Bakarat MT, Dean PM. Molecular structure matching by simulated annealing. III. The incorporation of null correspondences into the matching problem. J Comput Aided Mol Design 1991;5: 107-117.
15. Holm L, Sander C. DALI: a network tool for protein structure comparison. Trends Biochem Sci 1995;20:478-480.
16. Orengo CA, Brown NP, Taylor WR. Fast structure alignment for protein databank searching. Proteins 1992;14:139-167.
17. Alexandrov NN. SARFing the PDB. Prot Eng 1996;9:727-732.
18. Fischer D Tsai CJ, Nussinov R, Wolfson H. A 3D sequence-independent representation of the Protein Data Bank. Prot Eng 1995;8:981-997.
19. Sowdhamini R, Rufino SD, Blundell TL. A database of globular protein structural domains: clustering of representative family members into similar folds. Fold Design 1996;1:209-220.
20. Madej T, Gibrat JF, Bryant SH. Threading a database of protein cores. Proteins 1995;23:356-369.
21. Alexandrov NN, Fischer D. Analysis of topological and nontopological structural similarities in the PDB: new examples with old structures. Proteins 1996;25:354-365.
22. Alexandrov NN, Go N. Biological meaning, statistical significance, and classification of local spatial similarities in nonhomologous proteins. Prot Sci 1994;3:866-875.
23. Mizuguchi K, Go N. Comparison of spatial arrangements of secondary structure elements in proteins. Prot Eng 1995;8:353-362.
24. Rufino SD, Blundell TL. Structure-based identification and clustering of protein families and superfamilies. J Comput Aided Mol Design 1994;8:5-27.
25. Gibrat JF, Madej T, Bryant SH. Surprising similarities in structure comparison. Curr Opin Struct Biol 1996;6:377-385.
26. Holm L, Sander C. Touring protein fold space with Dali/FSSP. Nucleic Acids Res 1998;26:316-319.
27. Ohkawa H, Ostell J, Bryant S. MMDB: an ASN.1 specification for macromolecular structure. Ismb 1995;3:259-267.
28. Murzin AG, Brenner SE, Hubbard T, Chothia C. scop: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 1995;247:536-540.
29. 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.
30. Holm L, Sander C. Mapping the protein universe. Science 1996;273: 595-602.
31. Bemis G, Kuntz ID. A fast and efficient method for 2D and 3D molecular shape recognition. J Comput Aided Mol Design 1992;6: 607-628.
32. Richardson, JS. The anatomy and taxonomy of protein structure. Adv Prot Chem 1981;34:167-339.
33. Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983;22:2577-2637.
34. Willett P. Similarity and clustering in chemical information systems. New York: Wiley, 1987.
35. Boutonnet NS, Rooman MJ, Ochagavia ME, Richelle J, Wodak SJ. Optimal protein structure alignments by multiple linkage clustering: application to distantly related proteins. Prot Eng 1995;8:647-662.
36. Ryden L. Evolution of blue copper proteins. Prog Clin Biol Res 1988;274:349-366.
37. Ryden LG, Hunt LT. Evolution of protein complexity: the blue copper-containing oxidases and related proteins. J Mol Evol 1993; 1993;36:41-66.
38. Bork P, Sander C, Valencia A. An ATPase domain common to all prokaryotic cell cycle proteins, sugar kinases, actin, and hsp70 heat shock proteins. Proc Natl Acad Sci USA 1992;89:7290-7294.
39. Bryant, SH. Evaluation of threading specificity and accuracy. Proteins 1996;26:172-185.