Representing protein and peptide Structures with parallel-coordinates

Journal of Computational Chemistry

Volumn 18, Issue 15, 1997, Pages 1893-1902

  Becker, Oren M ^a  

^a TEL AVIV UNIVERSITY   (Israel)

Author keywords

Conformational analysis; Disulfide bonds; Parallel coordinates; Peptides; Proteins; Secondary structure; Visualization

Indexed keywords

EID: 0000997625     PISSN: 01928651     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1096-987X(19971130)18:15<1893::AID-JCC5>3.0.CO;2-J     Document Type: Article

References (34)

1. J. C. Hempel, R. M. Fine, M. Hassan, W. Ghoul, A. Guaragna, S. C. Koerber, Z. Li, and A. T. Hagler, Biopolymers, 36, 282 (1995).
2. A. E. Howard and P. A. Kollman, J. Med. Chem., 31, 1669 (1988).
3. A. R. Leach, In Reviews in Computational Chemistry, Vol. 2, K. B. Lipkowitz and D. B. Boyd, Eds., VCH, New York, 1991.
4. I. D. Kuntz, E. C. Meng, and B. K. Shoichet, Acc. Chem. Res., 27, 117 (1994).
5. A. Inselberg, T. Chomut, and M. Reif, J. Assoc. Comput. Mach., 34, 765 (1987).
6. A. Inselberg and B. Dimsdale, SIAM J. Appl. Math., 54, 559 (1994).
7. A. Inselberg and B. Dimsdale, SIAM J. Appl. Math, 54, 578 (1994).
8. J. C. Gower, Biometrika, 53, 325 (1966).
9. O. M. Becker, Proteins, 27, 213 (1997).
10. E. W. Basset, Ind. Comput., 14, 23 (1995).
11. B. T. Luke, J. Chem. Inf. Comput. Sci., 33, 135 (1993).
12. C. Branden and J. Tooze, Introduction to Protein Structure, Garland, New York, 1991.
13. C. L. Brooks III, M. Karplus, and B. M. Pettit, Proteins: A Theoretical Perspective of Dynamics, Structure and Thermodynamics, Vol. 71, John Wiley & Sons, New York, 1988.
14. F. H. Stillinger and T. A. Weber, Phys. Rev. A, 28, 2408 (1983).
15. R. E. Bruccoleri and M. Karplus, Biopolymers, 29, 1847 (1990).
16. Z. Li and H. A. Scheraga, Proc. Natl. Acad. Sci. USA, 84, 6611 (1987).
17. H. Meirovitch and E. Meirovitch, J. Comput. Chem., 18, 240 (1997).
18. O. M. Becker and M. Karplus, J. Chem. Phys., 106, 1495 (1997).
19. R. E. Kunz and R. S. Berry, J. Chem. Phys., 103, 1904 (1995); K. D. Ball et al., Science, 271, 963 (1996).
20. R. E. Kunz and R. S. Berry, J. Chem. Phys., 103, 1904 (1995); K. D. Ball et al., Science, 271, 963 (1996).
21. O. M. Becker, J. Mol. Struct. (THEOCHEM), 398-399, 507 (1997).
22. L. S. D. Caves, J. Evenseck, and M. Karplus, in press.
23. R. Abagyan and P. Argos, J. Mol. Biol., 225, 519 (1992).
24. J. M. Troyer and F. E. Cohen, Proteins. 23, 97 (1995).
25. R. Czerminski and R. Elber, J. Chem. Phys., 92, 5580 (1990).
26. E. G. Hutchinson and J. M. Thomton, Prof. Sci., 5, 212 (1996).
27. D. van der Spoel, B. L. De Groot, S. Hayward. H. J. C. Berendsen, and H. J. Vogel, Prot. Sci., 5, 2044 (1996).
28. W. Kabsch and C. Sander, Biopolymers, 22, 2577 (1983).
29. P. E. Smith, H. D. Blatt, and B. M. Pettit, Proteins, 27, 277 (1997).
30. C. N. Ramachandran, C. Ramakrishnan, and V. Sasisekharan, J. Mol. Biol., 7, 95 (1963).
31. J. M. Thornton, In Protein Folding, T. E. Creighton, Eds., W. H. Freeman, New York, 1992, p. 59.
32. C. Wilson, M. R. Wardell, K. H. Weisgraber, R. W. Mahley, and D. A. Agard, Science, 252, 1817 (1991).
33. M. Miller, J. Schneider, B. K. Sathyanarayana, M. V. Toth, G. R. Marshall, L. Clawson, L. Selk, S. B. H. Kent, and A. Wlodawer, Science, 246, 1149 (1989).
34. M. Marquart, J. Walter, J. Deisenhofer, W. Bode, and R. Huber, Acta Crystallogr. B, 39, 480 (1983).