Analysis of protein binding sites by computational solvent mapping

Methods in Molecular Biology

Volumn 819, Issue , 2012, Pages 13-27

  Hall, David R ^a   Kozakov, Dima ^a   Vajda, Sandor ^a  

^a Boston University   (United States)

Author keywords

Binding hot spots; Binding site; Binding site comparison; Docking; Druggability; Fragment based ligand design; Protein structure; Protein ligand interactions

Indexed keywords

PROTEIN; SOLVENT;

AMINO ACID SEQUENCE; ARTICLE; BINDING SITE; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER PROGRAM; HYDROGEN BOND; METABOLISM; METHODOLOGY; MOLECULAR GENETICS; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN DATABASE;

AMINO ACID SEQUENCE; BINDING SITES; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; HYDROGEN BONDING; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN BINDING; PROTEIN INTERACTION MAPPING; PROTEINS; SOFTWARE; SOLVENTS;

EID: 84855915978     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-465-0_2     Document Type: Article

References (19)

1. Clackson, T., and Wells, J.A. (1995) A hot spot of binding energy in a hormone-receptor interface. Science, 267, 383-386.
2. Mattos, C., and Ringe, D. (1996). Locating and characterizing binding sites on proteins. Nat. Biotechnol., 14, 595-599. (Pubitemid 26135122)
3. Hajduk, P. J., Huth, J. R., and Tse, C. (2005) Predicting protein druggability. Drug Discov Today 10, 1675-1682. (Pubitemid 41817616)
4. Hajduk, P.J., Huth, J. R., and Fesik, S. W. (2005). Druggability indices for protein targets derived from NMR-based screening data. J. Med. Chem. 48: 2518-2525. (Pubitemid 40516441)
5. Allen, K. N., Bellamacina, C. R., Ding, X., Jeffery, C. J., Mattos, C., Petsko, G. A, Ringe, D. (1996) An experimental approach to mapping the binding surfaces of crystalline proteins J. Phys. Chem. 100: 2605-2611, 1996. (Pubitemid 126793213)
6. English AC, Done SH, Caves LS, Groom CR, Hubbard RE. (1999) Locating interaction sites on proteins: the crystal structure of thermolysin soaked in 2% to 100% isopropanol. Proteins 37: 628-640.
7. English AC, Groom CR, Hubbard RE. (2001) Experimental and computational mapping of the binding surface of a crystalline protein. Protein Eng. 14: 47-59. (Pubitemid 32318937)
8. Mattos C, Bellamacina CR, Peisach E, Pereira A, Vitkup D, Petsko GA, Ringe D. (2006) Multiple solvent crystal structures: probing binding sites, plasticity and hydration. J Mol Biol. 357: 1471-1482.
9. Dennis S, Kortvelyesi T, Vajda S. (2002) Computational mapping identifies the binding sites of organic solvents on proteins. Proc. Natl. Acad. Sci. USA., 99: 4290-4295, 2002. (Pubitemid 34285978)
10. Brenke R, Kozakov D, Chuang G-Y, Beglov D, Hall D, Landon MR, Mattos C, Vajda S. (2009) Fragment-based identification of druggable "hot spots" of proteins using Fourier domain correlation techniques. Bioinformatics, 25: 621-627.
11. Silberstein M, Dennis S, Brown III L, Kortvelyesi T, Clodfelter K, Vajda S. (2003) Identification of substrate binding sites in enzymes by computational solvent mapping, J. Molec. Biol. 332: 1095-1113. (Pubitemid 37108802)
12. Landon MR, Lancia DR Jr, Yu J, Thiel SC, Vajda S. (2007) Identification of hot spots within druggable binding sites of proteins by computational solvent mapping. J. Med. Chem., 50: 1231-1240. (Pubitemid 46496323)
13. Vajda S, Guarnieri F. (2006) Characterization of protein-ligand interaction sites using experimental and computational methods. Current Opinion in Drug Design and Development 9: 354-362. (Pubitemid 43774164)
14. Landon MR, Lieberman RL, Hoang QQ, Ju S, Caaveiro JM, Orwig SD, Kozakov D, Brenke R, Chuang G-Y, Beglov D, Vajda S, Petsko GA, Ringe D. (2009) Detection of ligand binding hot spots on protein surfaces via fragment-based methods: application to DJ-1 and glucocerebrosidase, J Comput Aided Mol Des. 23: 491-500.
15. Landon MR, Amaro RE, Baron R, Ngan C-H, Ozonoff D, McCammon JA, Vajda S. (2008) Novel druggable hot spots in avian influenza neuraminidase H5N1 revealed by computational solvent mapping of a reduced and representative receptor ensemble, Chem Biol Drug Des 71: 106-116. (Pubitemid 351160979)
16. Ngan C-H, Beglov D, Rudnitskay AN, Kozakov D, Waxman DJ, and Vajda, S. (2009) The structural basis of pregnane X receptor binding promiscuity. Biochemistry, 48:11572-11581.
17. Chuang, G-Y., Kozakov, D., Brenke, R., Beglov, D., Guarnieri, F., and Vajda, S. (2009) Binding hot spots and amantadine orientation in the influenza a virus M2 proton channel. Biophys. J., 97(10): 2846-2853.
18. Congreve M, Aharony D, Albert J, Callaghan O, Campbell J, Carr RA, Chessari G, Cowan S, Edwards PD, Frederickson M, McMenamin R, Murray CW, Patel S, Wallis N. (2007) Application of fragment screening by X-ray crystallography to the discovery of aminopyridines as inhibitors of beta-secretase. J Med Chem 50:1124-1132. (Pubitemid 46496313)
19. Murray CW, Callaghan O, Chessari G, Cleasby A, Congreve M, Frederickson M, Hartshorn MJ, McMenamin R, Patel S, Wallis N. (2007) Application of fragment screening by X-ray crystallography to beta-secretase. J Med Chem 50:1116-1123. (Pubitemid 46496312)