Similarity measures based on gaussian-type promolecular electron density models: Alignment of small rigid molecules

Journal of Computational Chemistry

Volumn 27, Issue 15, 2006, Pages 1800-1816

  Leherte, Laurence ^a  

^a UNIVERSITY OF NAMUR   (Belgium)

Author keywords

Electrostatic energy; Endothiapepsin ligands; Kinetic operator; Molecular alignment; Promolecular electron density distribution; Similarity index; Smoothing

Indexed keywords

ELECTROSTATICS; GRAPHIC METHODS; KINETIC ENERGY; MATHEMATICAL MODELS; MOLECULAR ORIENTATION;

ENDOTHIAPEPSIN LIGANDS; KINETIC OPERATORS; PROMOLECULAR ELECTRON DENSITY (PED); SHAPE TANIMOTO INDEX; SIMILARITY INDICES;

ELECTRON DENSITY MEASUREMENT;

EID: 33750575142     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.20498     Document Type: Article

References (70)

1. Koritsanszky, T. S.; Coppens, Ph. Chem Rev 2001, 101, 1583.
2. Gironés, X.; Carbó-Dorca, R.; Mezey, P. G. J Mol Graph Model 2001, 19, 343.
3. Connolly, M. L. NetSci's Science Center: Computational Chemistry 1996. Available at http://www.netsci.org/Science/Compchem/feature14.html.
4. Good, A. C.; Richards, W. G. J Chem Inf Comput Sci 1993, 33, 112.
5. Grant, J. A.; Pickup, B. T. J Phys Chem 1995, 99, 3503.
6. Grant, J. A.; Gallardo, M. A.; Pickup, B. T. J Comput Chem 1996, 17, 1653.
7. Grant, J. A.; Pickup, B. T. Comput Simulat Biomol Syst 1997, 3, 150.
8. Nicholls, A.; MacGuish, N. E.; MacGuish, J. D. J Comput-Aided Mol Des 2004, 18, 451.
9. Maggiora, G. M.; Rohrer, D. C.; Mestres, J. J Mol Graph Model 2001, 19, 168.
10. Duncan, B. S.; Olson, A. J Biopolym 1993, 33, 231.
11. Tsirelson, V. G.; Avilov, A. S.; Abramov, Y. A.; Belokoneva, E. L.; Kitaneh, R.; Feil, D. Acta Crystallogr B 1998, 54, 8.
12. Tsirelson, V.; Abramov, Y.; Zavodnik, V.; Stash, A.; Belokoneva, E.; Stahn, J.; Pietsch, U.; Feil, D. Struct Chem 1998, 9, 249.
13. Gironés, X.; Amat, L.; Carbó-Dorca, R. J Mol Graph Model 1998, 16, 190.
14. Mitchell, A. S.; Spackman, M. A. J Comput Chem 2000, 21, 933.
15. Downs, R. T.; Gibbs, G. V.; Boisen, M. B., Jr.; Rosso, K. M. Phys Chem Miner 2002, 29, 369.
16. Irle, S.; Lin, H. L.; Niu, J. E.; Schwarz, W. H. E. Ber Bunsenges Phys Chem 1992, 96, 1545.
17. Aubert, E.; Porcher, F.; Souhassou, M.; Lecomte, Cl. Acta Crystallogr B 2003, 59, 687.
18. Spackman, M. A.; Maslen, E. N. J Phys Chem 1986, 90, 2020.
19. Maksic, Z. B.; Kovacek, D.; Vidic, B. Chem Phys Lett 1986, 129, 619.
20. Walker, P. D.; Mezey, P. G. J Am Chem Soc 1994, 116, 12022.
21. Exner, Th. E.; Mezey, P. G. J Comput Chem 2003, 24, 1980.
22. Whitehead, C. E.; Breneman, C. M.; Sukumar, N.; Ryan, M. D. J Comput Chem 2003, 24, 512.
23. Babu, K.; Gadre, S. R. J Comput Chem 2003, 24, 484.
24. Bader, R. W. Atoms in Molecules: A Quantum Theory; Clarendon Press: Oxford, 1995.
25. Gironés, X.; Amat, L.; Carbó-Dorca, R. J Chem Inf Comput Sci 2002, 42, 847.
26. Good, A. C.; Hodgkin, E. E.; Richards, W. G. J Chem Inf Comput Sci 1992, 32, 188.
27. Kostrowicki, J.; Piela, L.; Cherayil, B. J.; Scheraga, H. A. J Phys Chem 1991, 95, 4113.
28. Leherte, L.: Meurice, N.; Vercauteren, D. P. In Mathematics and Computers in Modern Science; Mastorakis, N., Ed.: World Scientific Engineering Society: Athens. 2000: pp. 158-164.
29. Leherte, L. J Math Chem 2001, 29, 47.
30. Leherte, L.; Meurice, N.; Vercauteren, D. P. J Comput-Aided Mol Des 2005, 19, 525.
31. Gadre, S. R.; Bhadane, P. K.; Pundlik, S. S.; Pingale, S. S. Mol Electrostat Potentials 1996, 3, 219.
32. Leboeuf, M.; Kösten A. M.: Jug, K.; Salahub, D. R. J Chem Phys 1999, 111, 4893.
33. Pathak, R. K.: Gadre, S. R. J Chem Phys 1990, 93, 1770.
34. Politzer, P.; Landry, S. J.: Wärnheim, T. J Phys Chem 1982, 86, 4767.
35. Sjoberg, P.; Politzer, P. J Phys Chem 1990, 94, 3959.
36. Pacios, L. F. J Phys Chem 1992, 96, 7294.
37. Botella, V.; Pacios, L. F. J Mol Struct (Theochem) 1998, 426, 75.
38. Amat, L.: Carbó-Dorca, R. J Chem Inf Comput Sci 2000, 40, 1188.
39. Amat, L.: Carbó-Dorca, R. J Comput Chem 1997, 18, 2023.
40. Coefficients and exponents can be downloaded from the Web site. Available at http://iqc.udg.es/cat/similarity/ASA/funcset.html.
41. Robert. D.; Carbó-Dorca. R. J Chem Inf Comput Sci 1998, 38, 469.
42. Maggiora, G. M.: Petke. J. D.: Mestres. J. J Math Chem 2002, 31, 251.
43. Willen, P. J Chem Inf Comput Sci 1998, 38, 983.
44. Cooper, D. L.; Allan. N. L. Understanding Chem React 1995, 14, 31.
45. McMurchie, L. E.; Davidson. E. R. J Comput Phys 1978, 26, 218-231.
46. Obara, S.; Saika. A. J Chem Phys 1986, 84, 3963.
47. McMahon, A. J.; King, P. M. J Comput Chem 1997, 18, 151.
48. Abramowitz. M.: Stegun, I. A. Handbook of Mathematical Functions with Formulas. Graphs, and Mathematical Tables: Dover: New York. 1970.
49. Leherte, L.: Dury, L.: Vereauteren, D. P. J Phys Chem A 2003, 107. 9875.
50. Hart, R. K.; Pappu, R. V.; Ponder. J. W. J Comput Chem 2000, 21, 531.
51. Bailey, D.; Cooper. J. B. Protein Sci 1994, 3, 2129.
52. Berman, H. M.; Westbrook, J.: Feng, Z.; Gilliland. G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E. Nucleic Acids Res 2000, 28, 235. Available at http://www.rcsb.org/pdb.
53. Lemmen, Ch.; Lengauer, Th.; Klebe, G. J Med Chem 1998, 41, 4502.
54. http://www.accelrys.com.
55. Solà, M.: Mestres, J.; Oliva, J. M.; Duran, M.; Carbó, R. Int J Quantum Chem 1996, 58, 361.
56. Guex, N.: Peitsch, M. C. Electrophoresis 1997, 18, 2714. Available at http://us.expasy.org/spdbv/.
57. Carugo, O. J Appl Crystallogr 2003, 36, 125.
58. DeLano, W. L. The PyMOL Molecular Graphics System;DeLano Scientific: San Carlos, CA, 2002. Available at http://www.pymol.org.
59. IBM Visualization Data Explorer. Available at http://www.opendx.org/.
60. Mestres, J.: Maggiora, G. M. J Math Chem 2006, 39, 107.
61. Masek, B. B.; Merchant, A.; Matthew, J. B. Proteins: Struct, Funct. Genet 1993, 193.
62. Walker, P. D.: Arteca, G. A.; Mezey, P. G. J Comput Chem 1993, 14, 1172.
63. Walker, P. D.; Mezey, P. G. J Comput Chem 1995, 16, 1238.
64. Klebe, G.; Mietzner, Th.; Weber. F. J Comput-Aided Mol Des 1999, 13, 35.
65. Glick, M.; Robinson, D. D.; Grant, G. H.; Richards. W. G. J Am Chem Soc 2002, 124, 2337.
66. Glick, M.; Grant. G. H.; Richards, W. G. J Med Chem 2002, 45, 4639.
67. Wang, K.; Murcia, M.; Constans, P.; Pérez. C.; Ortiz. A. R. J Comput-Aided Mol Des 2004, 18, 101.
68. Constans. P.; Amat. L.: Carbó-Dorca, R. J Comput Chem 1997, 18, 826.
69. Pappu, R. V.; Hart, R. K.; Ponder, J. W. J Phys Chem B 1998, 102, 9725.
70. Bultinck, P.; Kuppens, T.; Gironés, R.; Carbó-Dorca. R. J Chem Inf Comput Sci 2003. 43, 1143.