Three-dimensional threading approach to protein structure recognition

Polymer

Volumn 45, Issue 2, 2004, Pages 687-697

  Cao, Haibo ^a   Ihm, Yungok ^a   Wang, Cai Zhuang ^b   Morris, James R ^b   Su, Mehmet ^a   Dobbs, Drena ^a   Ho, Kai Ming ^a  

^a IOWA STATE UNIVERSITY   (United States)

^b IOWA STATE UNIVERSITY   (United States)

Author keywords

Alignment; Protein structure; Threading

Indexed keywords

COMPUTATIONAL METHODS; DATABASE SYSTEMS; EIGENVALUES AND EIGENFUNCTIONS; ITERATIVE METHODS; MATRIX ALGEBRA; MOLECULAR STRUCTURE; POLYMERS; VECTORS;

GAPPED STRUCTURAL THREADING METHOD; PROTEIN STRUCTURE PREDICTION;

PROTEINS;

PROTEIN;

AMINO ACID SEQUENCE; ANALYTIC METHOD; ARTICLE; MOLECULAR INTERACTION; PROTEIN ANALYSIS; PROTEIN STRUCTURE; SENSITIVITY AND SPECIFICITY; SEQUENCE HOMOLOGY; STRUCTURE ANALYSIS; THREE DIMENSIONAL IMAGING;

DATABASE; PROTEIN;

EID: 0345862083     PISSN: 00323861     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.polymer.2003.10.091     Document Type: Article

References (50)

1. Anfinsen C. Science 1973;181:223.
2. Murzin AG, Brenner SE, Hubbard T, Chothia C. J Mol Biol, 1995;247, 536-540.
3. (a) Dengler U, Siddiqui AS, Barton G. Proteins 2001;42:332-44.
4. (b) Siddiqui AS, Dengler U, Barton GJ. Bioinformatics 2001;17:200-1.
5. (a) Chandonia JM, Walker NS, Lo Conte L, Koehl P, Levitt M, Brenner SE. Nucl Acids Res 2002;30:260-3.
6. (b) Brenner SE, Koehl P, Levitt M. Nucl Acids Res 2000;28:254-6.
7. Altschul SF, Thomas LM, Alejandro AS, Zhang J, Zhang Z, Webb M, David JL. Nucl Acids Res 1997;25:3389-402.
8. Flory PJ. Principle of polymer chemistry. Ithaca, NY: Cornell University Press; 1953.
9. Ptitsyn OB, Kron AK, Yu Y, Eizner YY. J Polym Sci C 1968;16:3509.
10. de Gennes PG. J Phys Lett (Pairs) 1975;36:L55.
11. Post CB, Zimm BH. Biopolymers 1979;18:1487.
12. Sanchez IC. Macromolecules 1979;12:980.
13. Chan H, Dill KA. J Chem Phys 1990;92(5):3118.
14. Lau KF, Dill KA. Macromolecules 1989;22:3986.
15. Bryngelson JD, Onuchic JN, Socci ND, Wolynes PG. Proteins 1995;21:167-95.
16. Hendlich M, Lackner P, Weitckus S, Floechner H, Froschauer R, Gottsbachner K, Casari G, Sippl MJ. J Mol Biol 1990;216:167-80.
17. Bowie JU, Luthy R, Eisenberg D. Science 1991;253:164-70.
18. Jones DT, Taylor WR, Thomton JM. Nature 1992;358:86-9.
19. Sippl MJ, Weitckus S. Proteins 1992;13:258-71.
20. Godzik A, Kolinski A, Skolnick J. J Mol Biol 1992;227:227-38.
21. Ouzounis C, Sander C, Scharf M, Schneider R. J Mol Biol 1993;232:805-25.
22. Bryant SH, Lawrence CE. Proteins 1993;16:92-112.
23. Matsuo Y, Nishikawa K. Protein Sci 1994;3:2055-63.
24. Mirny LA, Shakhovich EI. J Mol Biol 1998;283:507-26.
25. Park BH, Levitt M. J Mol Biol 1996;258:367-92.
26. Park BH, Huang ES, Levitt M. J Mol Biol 1997;266:831-46.
27. Needleman SB, Wunsch CD. J Mol Biol 1970;48:443-53.
28. Smith TF, Waterman MS. J Mol Biol 1981;147:195-7.
29. Waterman MS, Eggert M. J Mol Biol 1987;197:723-8.
30. Miyazawa S, Jernigan RL. Protein Engng 2000;13:459-75.
31. Elofsson A, Fischer D, Rice DW, Le Grand S, Eisenberg D. Fold Design 1998;1:451-61.
32. Lathrop RH, Smith TF. J Mol Biol 1996;255:641-65.
33. Mirsky AE, Pauling L. Proc Natl Acad Sci USA 1936;22:439.
34. Kauzmann W. Adv Protein Chem 1959;14:1.
35. Miyazawa S, Jernigan RL. Macromolecules 1985;18:534-52.
36. Miyazawa S, Jernigan RL. J Mol Biol 1996;256:623-44.
37. Miyazawa S, Jernigan RL. Protein 1999;36:347-56.
38. Jones DT. J Mol Biol 1999;287:797-815.
39. Bryant SH, Altschul SF. Curr Opin Struct Biol 1995;5:236-44.
40. Li H, Tang C, Wingreen NS. Phys Rev Lett 1997;79:765-8.
41. Lau KF, Dill KA. Proc Natl Acad Sci USA 1990;87:638.
42. Shortle D, Chan H, Dill KA. Protein Sci 1992;1:201.
43. Press WH, Teukolsy SA, Vetterling WT, Flannery BP. Numerical recipes in fortran 77. New York: Cambridge University Press; 1999.
44. Meller J, Elber R. Proteins 2001;45:241-61.
45. Pierre B, Brunak S, Yves C, Claus AF. Bioinformatics 2000;5(16): 412-24.
46. The detail of CASP5 experiment is shown in the official CASP5 website: http://predictioncenter.llnl.gov/casp5/Casp5.html.
47. Fisher D, Elofsson A, Rice D, Eisenberg D. Pacific Symposium on Biocomputing, Hawaii; 1996. p. 300-18.
48. CAFASP-1: critical assessment of fully automated structure prediction methods Fischer D, Barret C, Bryson K, Elofsson A, Godzik A, Jones D, Karplus KJ, Kelley LA, Maccallum RM, Pawowski K, Rost B, Rychlewski L, Sternberg MJ. Proteins: Struct Funct Genet 1999;(Suppl. 3):209-17.
49. Rost B, Schneider N, Sander C. J Mol Biol 1997;270:471-80.
50. Luz JG, Hassig CA, Pickle C, Godzik A, Meyer BJ, Wilson IA. Genes Dev 2003;17:977.