Maximum feasibility guideline in the design and analysis of protein folding potentials

Journal of Computational Chemistry

Volumn 23, Issue 1, 2002, Pages 111-118

  Meller, Jaroslaw ^a,b   Wagner, Michael ^c   Elber, Ron ^a  

^a Department of Computer Science and School of Operations Research and Information Engineering   (United States)

^b NICOLAUS COPERNICUS UNIVERSITY   (Poland)

^c OLD DOMINION UNIVERSITY   (United States)

Author keywords

Folding potentials; Interior point methods; Linear programming

Indexed keywords

AMINO ACID; PROTEIN;

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; ELECTRICITY; METHODOLOGY; PROTEIN FOLDING;

ALGORITHMS; AMINO ACID SEQUENCE; AMINO ACIDS; COMPUTATIONAL BIOLOGY; ELECTROSTATICS; MODELS, MOLECULAR; PROTEIN FOLDING; PROTEINS;

EID: 0037079580     PISSN: 01928651     EISSN: None     Source Type: Journal    
DOI: 10.1002/jcc.10014     Document Type: Article

References (31)

1. 1 Maiorov, V. N. ; Crippen, G. M. J Mol Biol 1992, 227, 876.
2. 2 Vendruscolo, M. ; Domany, E. J Chem Phys 1998, 109, 11101.
3. 3 Tobi, D. ; Elber, R. Proteins Struct Funct Genet 2000, 41, 40.
4. 4 Tobi, D. ; Shafran, G. ; Linial, N. ; Elber, R. Proteins Struct Funct Genet 2000, 39, 71.
5. 5 Meller, J. ; Elber, R. Proteins 2001, 45, 241.
6. 6 Meller, J. ; Elber, R. Advances in Chemical Physics, in press.
7. 7 Akutsu, T. ; Tashimo, H. Proc. Pacific Symposium on Bio‐computing, 1998, p. 413.
8. 8 Sippl, M. J. ; Weitckus, S. Proteins 1992, 13, 258.
9. 9 Miyazawa, S. ; Jernigan, R. L. J Mol Biol 1996, 256, 623.
10. 10 Godzik, A. ; Kolinski, A. ; Skolnick, J. Proteins Struct Funct Genet 1996, 4, 363.
11. 11 Khachiyan, L. G. Doklady Akad Nauk USSR 1979, 244, 1093.
12. 12 Karmakar, N. K. Combinatorica 1984, 4, 373.
13. 13 Ye, Y. Interior Point Algorithms: Theory and Analysis ; Wiley: New York, 1997.
14. 14 Vanderbei, R. J. Linear Programming: Foundations and Extensions ; Kluwer Academic Publishers: New York, 1996.
15. 15 Wright, S. J. Primal‐Dual Interior‐Point Methods ; SIAM Publications: 1997.
16. 16 den Hertog, D. Interior Point Approach to Linear, Quadratic, and Convex Programming ; Kluwer Academic Publishers: New York, 1994.
17. 17 Adler, I. ; Monteiro, R. D. C. Math Program 1991, 50, 29.
18. 18 Monteiro, R. D. C. ; Adler, I. Math Program 1989, 44, 43.
19. 19 Chakravarti, N. Eur J Oper Res 1994, 73, 139.
20. 20 Parker, M. ; Ryan, J. Ann Math Artif Intell 1996, 17, 107.
21. 21 Chinneck, J. W. INFORMS J Comput 1997, 9, 164.
22. 22 Garey, M. R. ; Johnson, D. S. Computers and Intractability: A Guide to the Theory of NP‐Completeness ; W.H. Freeman and Company: New York, 1979.
23. 23 Meszaros, C. S. Comput Math Appl 1996, 31, 49.
24. 24 Hinds, D. A. ; Levitt, M. J Mol Biol 1994, 243, 668.
25. 25 Meller, J. ; Elber, R. http://www.tc.cornell.edu/CBIO/loopp.
26. 26 Liwo, A. ; Oldziej, S. ; Pincus, M. R. ; Wawak, R. J. ; Rackovsky, S. ; Scheraga, H. A. J Comput Chem 1997, 18, 849.
27. 27 Xia, Y. ; Huang, E. S. ; Levitt, M. ; Samudrala, R. J Mol Biol 2000, 300, 171.
28. 28 Yildrim, E. A. ; Wright, S. J. Technical Report 1258, School of Operations Res. and Industrial Eng., Cornell University.
29. 29 Chan, H. S. ; Dill, K. A. Proteins Struct Funct Genet 1998, 30, 2.
30. 30 Brown, G. ; Graves, G. Presented at ORSA/TIMS conference, Las Vegas, 1975.
31. 31 Chinneck, J. W. Ann Math Artif Intell 1996, 17, 127.