PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKaPredictions

Journal of Chemical Theory and Computation - Tập 7 Số 2 - Trang 525-537 - 2011
Mats H. M. Olsson1, Chresten R. Søndergaard1, Michał Rostkowski1, Jan H. Jensen1
1Department of Chemistry, University of Copenhagen, Universitetsparken 5, Copenhagen, Denmark

Tóm tắt

Từ khóa


Tài liệu tham khảo

Raquet X., 1997, Biophys. J., 73, 2416, 10.1016/S0006-3495(97)78270-5

Nielsen J. E., 2003, Protein Sci., 12, 1894, 10.1110/ps.03114903

Lamotte-Brasseur J., 1999, Protein Sci., 8, 404, 10.1110/ps.8.2.404

Lamotte-Brasseur J., 2000, Proteins, 40, 23, 10.1002/(SICI)1097-0134(20000701)40:1<23::AID-PROT40>3.0.CO;2-7

Warshel A., 1981, Biochemistry, 20, 3167, 10.1021/bi00514a028

Warshel A., 1981, Acc. Chem. Res., 14, 284, 10.1021/ar00069a004

Gunner M. R., 2006, Biochim. Biophys. Acta, Bioenerg., 1757, 942, 10.1016/j.bbabio.2006.06.005

Gunner M. R., 2000, Biochim. Biophys. Acta, Bioenerg., 1458, 63, 10.1016/S0005-2728(00)00060-8

Beroza P., 1998, Energ. Biol. Macromol., Part B, 295, 170, 10.1016/S0076-6879(98)95040-6

Warshel A., 1998, Curr. Opin. Struct. Biol., 8, 211, 10.1016/S0959-440X(98)80041-9

Ullmann G. M., 1999, Eur. Biophys. J. Biophys., 28, 533, 10.1007/s002490050236

Nielsen J. E., 2003, Protein Sci., 12, 313, 10.1110/ps.0229903

Mongan J., 2005, Curr. Opin. Struct. Biol., 15, 157, 10.1016/j.sbi.2005.02.002

Lee A. C., 2009, J. Chem. Inf. Model., 49, 2013, 10.1021/ci900209w

Davies M. N., 2006, BMC Biochem., 7, 10.1186/1471-2091-7-18

Stanton C. L., 2008, J. Chem. Theory. Comput., 4, 951, 10.1021/ct8000014

Li H., 2005, Proteins, 61, 704, 10.1002/prot.20660

Bas D. C., 2008, Proteins, 73, 765, 10.1002/prot.22102

Tanford C., 1957, J. Am. Chem. Soc., 79, 5333, 10.1021/ja01577a001

Warshel A., 1984, Proc. Natl. Acad. Sci., India, Sect. B, 81, 4785

Tanford C., 1972, Biochemistry, 11, 2192-&, 10.1021/bi00761a029

Mallik B., 2002, J. Comput. Chem., 23, 1090, 10.1002/jcc.10104

Schutz C. N., 2001, Proteins, 44, 400, 10.1002/prot.1106

Sham Y. Y., 1997, J. Phys. Chem. B, 101, 4458, 10.1021/jp963412w

Mehler E. L., 1999, Biophys. J., 77, 3, 10.1016/S0006-3495(99)76868-2

Jensen J. H., 2005, J. Phys. Chem. A, 109, 6634, 10.1021/jp051922x

Olsson M. H. M., 2003, J. Am. Chem. Soc., 125, 5025, 10.1021/ja0212157

Powers N., 2006, J. Biomol. NMR, 35, 39, 10.1007/s10858-006-9003-3

Forsyth W. R., 2002, Proteins, 48, 388, 10.1002/prot.10174

Song Y. F., 2009, J. Comput. Chem., 30, 2231, 10.1002/jcc.21222

pKacoop.http://amylase.ucd.ie/pKacoop(accessed Jan 1, 2011).

Hassan S. A., 2000, J. Phys. Chem. B, 104, 6490, 10.1021/jp9938967

Wisz M. S., 2003, Proteins, 51, 360, 10.1002/prot.10332

Simonson T., 2004, J. Am. Chem. Soc., 126, 4167, 10.1021/ja039788m

Pokala N., 2004, Protein Sci., 13, 925, 10.1110/ps.03486104

Georgescu R. E., 2002, Biophys. J., 83, 1731, 10.1016/S0006-3495(02)73940-4