Who cares for the protons?

Bioorganic and Medicinal Chemistry

Volumn 20, Issue 18, 2012, Pages 5453-5460

  Czodrowski, Paul ^a  

^a MERCK KGAA   (Germany)

Author keywords

BIPS; Drug design; pKa calculation; Protonation

Indexed keywords

LINAGLIPTIN; PROTON; RILPIVIRINE; RIVAROXABAN; ROFLUMILAST; VANDETANIB;

ANALYTIC METHOD; ARTICLE; CHEMICAL ANALYSIS; CHEMICAL STRUCTURE; MULTI CONFORMATION CONTINUUM ELECTROSTATICS; PROPKA METHOD; PROTON TRANSPORT;

HYDROGEN-ION CONCENTRATION; LIGANDS; PHARMACEUTICAL PREPARATIONS; PROTEINS; PROTONS;

EID: 84866244865     PISSN: 09680896     EISSN: 14643391     Source Type: Journal    
DOI: 10.1016/j.bmc.2012.03.009     Document Type: Article

References (30)

1. C.R. Sondergaard, M. Olsson, M. Rostkowski, and J.H. Jensen J. Chem. Theory Comput. 7 2011 525
2. Y. Song, J. Mao, and M.R. Gunner J. Comput. Chem. 30 2009 2231
3. M.N. Davies, C.P. Toseland, D.S. Moss, and D.R. Flower BMC Biochem. 7 2006 18
4. C.L. Stanton, and K.N. Houk J. Chem. Theory Comput. 4 2008 951
5. P. Czodrowski Proteins: Structure, Function, and Bioinformatics 79 2011 3299
6. Maestro version 9.2, Schrodinger LLC, New York, NY, USA 2011.
7. M. Eckhardt, E. Langkopf, M. Mark, M. Tadayyon, L. Thomas, H. Nar, W. Pfrengle, B. Guth, R. Lotz, P. Sieger, H. Fuchs, and F. Himmelsbach J. Med. Chem. 50 2007 6450
8. S. Roehrig, A. Straub, J. Pohlmann, T. Lampe, J. Pernerstorfer, K.-h. Schlemmer, P. Reinemer, and E. Perzborn J. Med. Chem. 48 2005 5900 5908
9. K. Das, J.D. Bauman, A.D. Clark, Y.V. Frenkel, P.J. Lewi, A.J. Shatkin, S.H. Hughes, and E. Arnold Proc. Natl. Acad. Sci. U.S.A. 105 2008 1466
10. G.L. Card, B.P. England, Y. Suzuki, D. Fong, B. Powell, B. Lee, C. Luu, M. Tabrizizad, S. Gillette, P.N. Ibrahim, D.R. Artis, G. Bollag, M.V. Milburn, S.-H. Kim, J. Schlessinger, and K.Y.J. Zhang Structure 12 2004 2233
11. P.P. Knowles, J. Murray-Rust, S. Kjaer, R.P. Scott, S. Hanrahan, M. Santoro, C.F. Ibáñez, and N.Q. McDonald J. Biol. Chem. 281 2006 33577
12. PRIME 3.0, Schrodinger LLC, New York, NY, USA 2011.
13. P. Czodrowski, I. Dramburg, C.A. Sotriffer, and G. Klebe Proteins: Structure, Function, and Bioinformatics 65 2006 424
14. J. Wang, R.M. Wolf, J.W. Caldwell, P.A. Kollman, and D.A. Case J. Comput. Chem. 25 2004 1157
15. pKalc 4.3.0, CompuDrug, Sedona, AZ, USA 2011.
16. A. Warshel Biochemistry 20 1981 3167 3177
17. C.N. Schutz, and A. Warshel Proteins: Structure, Function, and Bioinformatics 44 2001 400
18. A.R. Klingen, E. Bombarda, and G.M. Ullmann Photochem. Photobiol. Sci. 5 2006 588
19. C.R. Sondergaard, L.P. McIntosh, G. Pollastri, and J.E. Nielsen J. Mol. Biol. 376 2008 269
20. L.P. McIntosh, G. Hand, P.E. Johnson, M.D. Joshi, M. Körner, L.A. Plesniak, L. Ziser, W.W. Wakarchuk, and S.G. Withers Biochemistry 35 1996 9958
21. J. Qin, G.M. Clore, and a.M. Gronenborn Biochemistry 35 1996 7
22. H. Webb, B.M. Tynan-Connolly, G.M. Lee, D. Farrell, F. O'Meara, C.R. Sondergaard, K. Teilum, C. Hewage, L.P. McIntosh, and J.E. Nielsen Proteins 79 2011 685
23. L. Tambuyzer, H. Azijn, L.T. Rimsky, J. Vingerhoets, P. Lecocq, G. Kraus, G. Picchio, and M.-P. de Béthune Antivir. Ther. 14 2009 103
24. L.B. Johnson, and L.D. Saravolatz Clin. Infect. Dis. 48 2009 1123
25. H. Steuber, P. Czodrowski, C.A. Sotriffer, and G. Klebe J. Mol. Biol. 373 2007 1305
26. P. Czodrowski, C.A. Sotriffer, and G. Klebe J. Mol. Biol. 367 2007 1347
27. H. Guo, A. Wlodawer, T. Nakayama, Q. Xu, and H. Guo Biochemistry 45 2006 9129
28. D. Narzi, S.W.I. Siu, C.U. Stirnimann, J.P.a. Grimshaw, R. Glockshuber, G. Capitani, and R.a. Böckmann J. Mol. Biol. 382 2008 978
29. M. Rostkowski, M.H.M. Olsson, C.R. Sondergaard, and J.H. Jensen BMC Struct. Biol. 11 2011 6
30. K. Stierand, P.C. Maass, and M. Rarey Bioinformatics (Oxford, England) 22 2006 1710 (http://www.poseview.de)