Computing ionization states of proteins with a detailed charge model

Journal of Computational Chemistry

Volumn 17, Issue 14, 1996, Pages 1633-1644

  Antosiewicz, Jan ^a,b   Briggs, James M ^a   Elcock, Adrian H ^a   Gilson, Michael K ^a,c   Mccammon, J Andrew ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF WARSAW   (Poland)

^c NATIONAL INSTITUTE OF STANDARDS AND TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0000945505     PISSN: 01928651     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1096-987X(19961115)17:14<1633::AID-JCC5>3.0.CO;2-M     Document Type: Article

References (37)

1. D. Bashford and M. Karplus, Biochemistry, 29, 10219-10225 (1990).
2. D. Bashford and M. Karplus, J. Phys. Chan., 95, 9556-9561 (1991).
3. C. Lim, D. Bashford, and M. Karplus, J. Phys. Chem., 95, 5610-5620 (1991).
4. A.-S. Yang, M. R. Gunner, R. Sampogna, K. Sharp, and B. Honig, Prot. Struct. Funct. Genet., 15, 252-265 (1993).
5. J. Antosiewicz, J. A. McCammon, and M. K. Gilson, J. Mol. Biol., 238, 415-436 (1994).
6. M. K. Gilson and B. H. Honig, Biopolymers, 25, 2097-2119 (1986).
7. T. Simonson, D. Perahia, and A. T. Brunger, Biophys. J., 59, 670-690 (1991).
8. P. E. Smith, R. M. Brunne, A. E. Mark, and W. F. van Gunsteren, J. Phys. Chem., 97, 2009-2014 (1993).
9. J. Warwicker and H. C. Watson, J. Mol. Biol., 157, 671-679 (1982).
10. M. E. Davis, J. D. Madura, B. A. Luty, and J. A. McCammon, Comp. Phys. Commun., 62, 187-197 (1991).
11. J. D. Madura, J. M. Briggs, R. C. Wade, M. E. Davis, B. A. Luty, A. Ilin, J. Antosiewicz, M. K. Gilson, B. Bagheri, L. R. Scott, and J. A. McCammon, Comput. Phys. Commun., 91, 57 (1995).
12. D. Bashford and K. Gerwert, J. Mol. Biol., 224, 473-486 (1992).
13. F. C. Bernstein, T. F. Koettzle, G. J. B. Williams, E. F. Meyer, M. D. Brice, J. R. Rodgers, O. Kennard, T. Shimanouchi, and M. J. Tasumi, J. Mol. Biol., 123, 557-594 (1977).
14. C. Tanford and J. G. Kirkwood, J. Am. Chem. Soc., 79, 5333-5339 (1957).
15. D. Bashford and M. Karplus, Biochemistry, 9, 327-335 (1990).
16. M. K. Gilson, Proteins, 15, 266-282 (1993).
17. J. A. Schellman, Biopolymers, 14, 999-1018 (1975).
18. J. Antosiewicz and D. Porschke, Biophys. J., 68, 655-664 (1995).
19. J. Antosiewicz and D. Porschke, Biochemistry, 28, 10077-10078 (1989).
20. P. Beroza, D. R. Fredkin, M. Y. Okamura, and G. Feher, Proc. Natl. Acad. Sci. USA, 88, 5804-5808 (1991).
21. D. Bashford, D. A. Case, C. Dalvit, L. Tennant, and P. E. Wright, Biochemistry, 32, 8045-8056 (1993).
22. N. Metropolis, A. W. Rosenbluth, M. N. Rosenbluth, A. H. Teller, and E. Teller, J. Chem. Phys., 21, 1087-1092 (1953).
23. M. Ramanadham, L. C. Sieker, and L. H. Jensen, Acta Crystallogr. (Sect. A), 37C, 33 (1981).
24. M. Marquart, J. Walter, J. Desenhofer, W. Bode, and R. Huber, Acta Crystallogr. (Sect. B), 39, 480 (1983).
25. W. Bode, A.-Z. Wei, R. Huber, E. Meyer, J. Travis, and S. Neumann, EMBO J., 5, 2453-2458 (1986).
26. B. Howlin, D. S. Moss, and G. W. Harris, Acta Crystallogr. (Sect. A), 45, 851 (1989).
27. D. Sitkoff, K. A. Sharp, and B. Honig, J. Phys. Chem., 98, 1978-1988 (1994).
28. F. M. Richards, Ann. Rev. Biophys. Bioeng., 6, 151-176 (1977).
29. M. K. Gilson, K. A. Sharp, and B. H. Honig, J. Comput. Chem., 9, 327-335 (1988).
30. A. T. Brunger and M. Karplus, Prot. Struct. Funct. Genet., 4, 148-156 (1988).
31. B. R. Brooks, R. E. Bruccoleri, B. D. O. D. J. States, S. Swaminathan, and M. Karplus, J. Comput. Chem., 4, 187-217 (1982).
32. K. Bartik, C. Redfield, and C. M. Dobson, Biophys. J., 66, 1180-1184 (1994).
33. L. R. Brown, A. D. Marco, G. Wagner, and K. Wüthrich, Eur. J. Biochem., 62, 103-107 (1976).
34. L. R. Brown, A. D. Marco, R. Richarz, G. Wagner, and K. Wüthrich, Eur. J. Biochem., 88, 87-95 (1978).
35. R. Richarz and K. Wüthrich, Biochemistry, 17, 2263-2269 (1978).
36. W. Schaller and A. D. Robertson, Biochemistry, 34, 4714-4723 (1995).
37. 1H NMR, in C. M. Cuchillo, R. de Llorens, M. V. Nogués, and X. Parés, Eds., Structure, Mechanism and Function of Ribonucleases. Proceedings of the 2nd International Meeting, Held in Sant Feliu de Guíxols, Girona, Spain, 1990, pp. 9-14, Bellaterra, Spain, Departement de Bioquímica i Biologia Molecular and Institut de Biologia Fonamental Vicent Villar Palasí, Universitat Autònoma de Barcelona, 1991.