Neighbor-list reduction: Optimization for computation of molecular van der Waals and solvent-accessible surface areas

Journal of Computational Chemistry

Volumn 19, Issue 7, 1998, Pages 797-808

  Weiser, Jörg ^a   Weiser, Armin A ^a,b   Shenkin, Peter S ^a   Still, W Clark ^a  

^a Columbia University ^*  (United States)

^b TECHNISCHE UNIVERSITÄT BERLIN   (Germany)

Author keywords

Neighbor list; Protein structures; Solvent accessible surface area (SASA), numerical calculation; United And all atom representations; Van der Waals surface area (vdWSA)

Indexed keywords

EID: 0001229337     PISSN: 01928651     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1096-987X(199805)19:7<797::AID-JCC9>3.0.CO;2-L     Document Type: Article

References (33)

1. B. Lee and F. M. Richards, J. Mol. Biol., 55, 379 (1971).
2. R. B. Hermann, J. Phys. Chem., 76, 2754 (1972).
3. A. Shrake and J. A. Rupley, J. Mol. Biol., 79, 351 (1973).
4. T. J. Richmond and F. M. Richards, J. Mol. Biol., 119, 537 (1978).
5. W. Kabsch and C. Sander, Biopolymers, 22, 2577 (1983).
6. H. Wang and C. Levinthal, J. Comput. Chem., 12, 868 (1991).
7. S. M. Le Grand and K. M. Merz Jr., J. Comput. Chem., 14, 349 (1993).
8. R. Abagyan, M. Totrov, and D. Kuznetsov, J. Comput. Chem., 15, 488 (1994)
9. F. Eisenhaber, P. Lijnzaad, P. Argos, C. Sander, and M. Scharf, J. Comput. Chem., 16, 273 (1995).
10. (a) A. A. Bliznyuk and J. E. Gready, J. Comput. Chem., 17, 962 (1996);
11. (b) A. A. Bliznyuk and J. E. Gready, J. Comput. Chem., 17, 970 (1996).
12. S. J. Wodak and J. Janin, Proc. Natl. Acad. Sci. USA, 77, 1736 (1980).
13. T. J. Richmond, J. Mol. Biol., 178, 63 (1984).
14. W. Hasel, T. F. Hendrickson, and W. C. Still, Tetrahed. Comput. Meth., 1, 103 (1988).
15. L. R. Dodd and D. N. Theodorou, Mol. Phys., 72, 1313 (1991).
16. L. Wesson and D. Eisenberg, Prof. Sci., 1, 227 (1992).
17. G. Perrot, B. Cheng, K. D. Gibson, J. Vila, K. A. Palmer, A. Nayeem, B. Maigret, and H. A. Scheraga, J. Comput. Chem., 13, 1 (1992).
18. B. von Freyberg and W. Braun, J. Comput. Chem., 14, 510 (1993).
19. F. Eisenhaber and P. Argos, J. Comput. Chem., 14, 1272 (1993).
20. M. Petitjean, J. Comput. Chem., 15, 507 (1994).
21. D. A. Liotard, G. D. Hawkins, G. C. Lynch, C. J. Cramer, and D. G. Truhlar, J. Comput. Chem., 16, 422 (1995).
22. S. Sridharan, A. Nicholls, and K. A. Sharp, J. Comput. Chem., 16, 1038 (1995).
23. M. F. Sanner, A. J. Olson, and J.-C. Spehner, Biopolymers, 38, 305 (1996).
24. R. R. Gabdoulline and R. C. Wade, J. Mol. Graph., 14, 341 (1996).
25. K. D. Gibson and H. A. Scheraga, Mol. Phys., 62, 1247 (1987).
26. S. J. Hubbard and J. M. Thornton, NACCESS (Version 2.0) Computer Program, Department of Biochemistry and Molecular Biology, University College London, 1993. The source is available via http://www.biochem.ucl.ac.uk/≃ roman/naccess/naccess.html.
27. C, but Q is substituted by G; see Fig. 4), includes G and C. If this is the case, then eliminate j from Full4[i] and eliminate i from Full4[j].
28. F. Mohamadi, N. G. J. Richards, W. C. Guida, R. Liskamp, M. Lipton, C. Caufield, G. Chang, T. Hendrickson, and W. C. Still, J. Comput. Chem. 11, 440 (1990). (We used MacroModel, version 6.0.)
29. F. C. Bernstein, T. F. Koetzle, G. J. B. Williams, E. F. Meyer Jr., M. D. Brice, J. R. Rodgers, O. Kennard, T. Shimanouchi, and M. Tasumi, J. Mol. Biol. 112, 535 (1977).
30. J. D. Augspurger and H. A. Scheraga, J. Comput. Chem., 17, 1549 (1996).
31. (a) J. A. Grant and B. T. Pickup, J. Phys. Chem. 99, 3503 (1995).
32. (b) J. A. Grant, M. A. Gallardo, and B. T. Pickup, J. Comput. Chem. 17, 1653 (1996).
33. P. F. W. Stouten, C. Frömmel, H. Nakamura, and C. Sander, Mol. Simul., 10, 97 (1993).