Molecular shape and electrostatics in the encoding of relevant chemical information

Journal of Computer-Aided Molecular Design

Volumn 19, Issue 9-10, 2005, Pages 661-686

  Nicholls, Anthony ^a   Grant, J Andrew ^b  

^a OpenEye Scientific Software Inc   (United States)

^b ASTRAZENECA   (United Kingdom)

Author keywords

Analytic representation; Database storage; Electrostatics; Molecular encoding; Molecular shape; QSAR; Shape fingerprints; Similarity

Indexed keywords

COMPUTATIONAL CHEMISTRY; DISSOCIATION; ENCODING (SYMBOLS); MOLECULES; SIGNAL ENCODING;

ANALYTIC REPRESENTATION; CHEMICAL INFORMATION; DATABASE STORAGE; ENCODINGS; MOLECULAR ENCODING; MOLECULAR SHAPES; PROPERTY; QSAR; SHAPE-FINGERPRINTS; SIMILARITY;

ELECTROSTATICS;

ACETYLSALICYLIC ACID; CYCLIN DEPENDENT KINASE 6; ENZYME INHIBITOR; FESITIN; OMEPRAZOLE; UNCLASSIFIED DRUG;

ARTICLE; CHEMICAL ENGINEERING; COMPUTER AIDED DESIGN; COMPUTER MODEL; COMPUTER PROGRAM; DATA BASE; DRUG DESIGN; DRUG RESEARCH; DRUG STRUCTURE; ELECTRIC ACTIVITY; ELECTROCHEMISTRY; INFORMATION SYSTEM; MATHEMATICAL COMPUTING; MOLECULAR COMPUTER; MOLECULAR SIZE; PRIORITY JOURNAL; QUANTITATIVE STRUCTURE ACTIVITY RELATION; STRUCTURE ANALYSIS;

EID: 33644510432     PISSN: 0920654X     EISSN: 15734951     Source Type: Journal    
DOI: 10.1007/s10822-005-9019-x     Document Type: Article

References (43)

1. Hohenberg P., Kohn W., (1964) Phys. Rev. B, 136:864
2. Bissantz C., Folkers G., Rognan D., (2000) J. Med. Chem. 43: 4759
3. Nicholls A., MacCuish N.E., MacCuish J.D., (2004) JCAMD, 18: 451
4. Rush T.S., Grant J.A., Mosyak L., Nicholls A., (2005) J. Med. Chem. 48(5): 1489
5. Katz, A.H., Tawa, G.J., Mason, K., Gove, S. and Alvarez, J.C., Comput. Chem., 92 (2004), ACS, Anaheim
6. Tawa, G.J., Katz, A.H. and Alvarez, J.C., Comput. Chem., 244 (2004) ACS, Philadelphia
7. Petit-Zeman, S., 4th Horizon Symposium, Oct. 23-25, 2003
8. Bohacek R.S., McMartin C., Guida W.C., (1996) Med. Res. Rev. 16: 3
9. Masek B.B, Merchant A., Matthews J.B., (1993) Proteins 17: 193
10. Grant J.A., Pickup B.T., (1995) J. Phys. Chem. 99: 3503
11. Grant J.A., Pickup B.T., (1996) J. Comput. Chem, 17: 1653
12. Grant, J.A., Haigh, J.A., Nicholls, A. and Pickup, B.T., JCICS, Vol. 20, (2005) (In press)
13. Nicholls, A., Daylight Users Group Meeting, Feb. 24-27th, 1998
14. Hall, D.W. and Spencer, G.L., Elementary Topology, Wiley, 1955, p. 59ff
15. Fink T., Bruggesser H., Reymond J.-L, 2005 Angew. Chem. Int. Ed. 44: 1504
16. Putta S., Christian L., Beroza P., Greene J., 2002 JCICS 42: 1230
17. Kearsley S.K., Smith G.M., (1990) Tet. Comp. Met 3: 615
18. Good A.C., Hodgkin E.E., Richards W.G., (1992) JCICS. 32: 188
19. Good A.C., Richards W.G., (1993) J. Chem. Inf. Comput. Sci., 33: 112
20. Lin, J.-H. and Clark, T., J. Chem. Inf. Model (2005) 45 (in press)
21. Kazhdan, M.M., Thesis Dissertation, Comp. Sci. Dept., Princeton, June 2004
22. Duncan B.S., Olson A.J, 1993 Biopolymers 33: 219
23. Leicester S.E., Finney J.L., Bywater R.P, 1988 J. Mol. Graphics 6: 104
24. Max N.L., Getzoff E.D., 1988 IEEE Comput. Graphics Appl. 8: 42
25. Ritchie, D.W. and Kemp, G.J., Proteins: Structure, Function & Genetics, John Wiley & Sons, 1999
26. Ritchie D.W., Kemp G.J.L., 1999 J. Comput. Chem. 20(4): 383
27. Grant, J.A. and Pickup, B.T., In W. Gunsteren and P.K. Weiner (Eds.), Computer Simulation of Biomolecular Systems, Vol. 3, Kluwer, 1997
28. Perola E., Charifson P., (2004) J. Med. Chem. 47:2499
29. Boström J., Norby P.-O., Liljefors T., (1998) JCAMD 12:383
30. ROCS 2.0, Omega 1.1, WABE 0.9, EON 1.0, OpenEye Scientific Software, Santa Fe, NM (www.eyesopen.com)
31. Bostrom J., Greenwood J.R., Gottfries J., (2003) J. Mol. Graph Model 5:449
32. Gasteiger, J. and Marsili, M., Tetrahedron Lett. (1978) 3181
33. Durant J.L., Leland B.A., Henry D.R., Nourse J.G., (2002) J. Chem. Inf. Comput. Sci., 42: 1273
34. Fingerprint, M., Mesa Analytics & Computing, LLC, Santa Fe, NM, www.mesaac.com
35. Lu H., Chang D.J., Baratte B., Meijer L., Schulze-Gahmen U., (2005) J. Med. Chem. 48: 737
36. MDDR (MDL Drug Data Report), MDL, Inc and Prous Science (1995-2005)
37. Corina, Molecular Networks, GmbH Computerchemie Langemarckplatz 1, Erlangen, Germany
38. Jones, H. Thesis Dissertation, Chemistry Dept., University of Sheffield, 2004
39. Smith D.J., Forrest S., Hightower R.R., Perelson A.S., (1997) J. Theor. Biol. 189: 141
40. Lapedes, A. and Farber R., Santa Fe Institute working paper 00-01-006
41. Abagyan, R., Raush, E. and Budagyan, L. Safe Exchange of Chemical Information Symposium, March 14th 2005, San Diego, ACS
42. vonNeumann, J. and Morgenstern, O., Theory of Games and Economic Behavior, Princeton Univ. Press, 1944
43. Schneier, B., Applied Cryptography, Wiley, 1995