Computational methods for the structural alignment of molecules

Journal of Computer-Aided Molecular Design

Volumn 14, Issue 3, 2000, Pages 215-232

  Lemmen, Christian ^a,b   Lengauer, Thomas ^a  

^a FRAUNHOFER INSTITUTE FOR APPLIED INFORMATION TECHNOLOGY FIT   (Germany)

^b Formerly CombiChem Inc   (United States)

Author keywords

Computational methods; Review; Structural alignment

Indexed keywords

BINDING ENERGY; COMPUTATIONAL CHEMISTRY; COMPUTATIONAL METHODS; MOLECULES; REVIEWS;

3D-QSAR; BINDING AFFINITIES; BINDING GEOMETRIES; DRUG DESIGN; PHARMACOPHORES; QSAR STUDIES; RECEPTOR MODELING; RECEPTORS PROTEINS; STRUCTURAL ALIGNMENTS; STRUCTURAL INFORMATION;

LIGANDS;

LIGAND; RECEPTOR PROTEIN;

BINDING AFFINITY; CONTROLLED STUDY; DATA BASE; DRUG DESIGN; INTERMETHOD COMPARISON; METHODOLOGY; MOLECULE; PHARMACOPHORE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN STRUCTURE; QUANTITATIVE STRUCTURE ACTIVITY RELATION; REVIEW; SCREENING; STRUCTURE ANALYSIS;

EID: 0034065350     PISSN: 0920654X     EISSN: None     Source Type: Journal    
DOI: 10.1023/A:1008194019144     Document Type: Review

References (142)

1. Brint, A.T. and Willett, P., J. Chem. Inf. Comput. Sci., 27 (1987) 152.
2. Martin, Y.C., Bures, M.G. and Willett, P., In Lipkowitz, B. and Boyd, D.B., Reviews in Computational Chemistry, VCH, Weinheim, 1990, pp. 265-294.
3. Kubinyi, H. (Ed.) 3D QSAR in Drug Design. Theory, Methods and Applications. ESCOM, Leiden, 1993.
4. Golender, V.E. and Vorpagel., E.R., In Kubinyi, H. (Ed.) 3D QSAR in Drug Design. Theory, Methods and Applications. ESCOM, Leiden, 1993, pp. 137-149.
5. Wermuth, C.-G. and Langer, T., In Kubinyi, H. (Ed.) 3D QSAR in Drug Design. Theory, Methods and Applications. ESCOM, Leiden, 1993, pp. 117-136.
6. Kabsch, W., Acta Crystallogr., A32 (1976) 922.
7. Redington, P.K., Comput. Chem., 16 (1992) 217.
8. Hurst, T., J. Chem. Inf. Comput. Sci., 34 (1994) 190.
9. Carbó, R., Leyda, L. and Arnau, M., Int. J. Quant. Chem., 17 (1980) 1185.
10. Hodgkin, E.E. and Richards, G., Int. J. Quant. Chem., Quantum Biol. Symp., 14 (1987) 105.
11. Lamdan, Y. and Wolfson, H.J., IEEE International Conference on Computer Vision, Tampa, FL, 1988, pp. 238-249.
12. Nussinov, R. and Wolfson, H.J., Proc. Natl. Acad. Sci. USA, 88 (1991) 10495.
13. Martin, Y.C., Bures, M.G., Danaher, E.A., DeLazzer, J., Lico, I. and Pavlik, P.A., J. Comput.-Aided Mol. Design, 7 (1992) 83.
14. Bron, C. and Kerbosch, J., Communications of the ACM, 16 (1973) 575.
15. Crippen, G.M. and Havel, T.F., Distance Geometry and Molecular Conformation. Research Studies Press, Taunton, 1988.
16. Devillers, J. (Ed.) Genetic Algorithms in Molecular Modelling. Academic Press, London, 1996.
17. Kearsley, S.K. and Smith, G.M., Tetrahedron Comput. Methodol., 3 (1990) 615.
18. Johnson, M.A. and Maggiora, G.M. (Eds) Concepts and Applications of Molecular Similarity. John Wiley & Sons, New York, NY, 1990.
19. Dean, P.M., In Dean, P.M. (Ed.) Molecular Similarity in Drug Design. Blackie Academic & Professional, London, 1995, pp. 1-23.
20. Good, A.C., In Dean, P.M. (Ed.) Molecular Similarity in Drug Design. Blackie Academic & Professional, London, 1995, pp. 24-56.
21. Rouvray, D.H., In Sen, K. (Ed.) Molecular Similarity I. Topics in Current Chemistry, Vol. 173, Springer-Verlag, Heidelberg, 1995, pp. 1-30.
22. Klopman, G., J. Am. Chem. Soc., 106 (1984) 7315.
23. Klopman, G., Quant. Struct.-Act. Relat., 11 (1992) 176.
24. Petke, J.D., J. Comput. Chem., 14 (1993) 928.
25. Crippen, G.M., J. Comput. Chem., 16 (1995) 486.
26. Ghose, A.K. and Crippen, C.M., In Ramsden, C. (Ed.) Comprehensive Medicinal Chemistry: the Rational Design, Mechastic Study, and Therapeutic Application of Chemical Compounds. Vol. 4. Pergamon Press, Oxford, 1990, pp. 715-753.
27. Crippen, G.M., J. Comput. Chem., 8 (1987) 943.
28. Gasteiger, J. and Li, X., Angew. Chem. Int. Ed. Engl., 33 (1994) 643.
29. Gasteiger, J. and Zupan, J., Biol. Cybern., 70 (1993) 189.
30. Polański, J., Gasteiger, J., Wagener, M. and Sadowski, J., Quant. Struct.-Act. Relat., 17 (1998) 27.
31. Apaya, R.P., Luchese, B., Price, S.L. and Vinter, J.G., J. Comput.-Aided Mol. Design, 9 (1995) 33.
32. Blanley, F.E., Edge, C. and Phippen, R.W., J. Mol. Graph., 13 (1995) 165.
33. Robinson, D.D., Lyne, P.D. and Richards, W.G., J. Chem. Inf. Comput. Sci., 39 (1999) 594.
34. Mezey, P.G., In Dean, P.M. (Ed.) Molecular Similarity in Drug Design. Blackie Academic & Professional, London, 1995, pp. 241-268.
35. Matter, H. and Rarey, M., In Jung, G. (Ed.) Combinatorial Organic Chemistry. John Wiley & Sons, New York, NY, 1999.
36. Humblet, C. and Dunbar Jr., J.B., In Venuti, M.C. (Ed.) Annual Reports in Medicinal Chemistry. Vol. 28, Chapter VI. Topics in Drug Design and Discovery. Academic Press, London, 1993, pp. 275-284.
37. Willett, P., J. Mol. Recognition, 8 (1995) 290.
38. Brown, R.D. and Martin, Y.C., J. Chem. Inf. Comput. Sci., 36 (1996) 572.
39. Lauri, G. and Bartlett, P.A., J. Comput.-Aided Mol. Design, 8 (1993) 51.
40. Bartlett, P.A., Shea, G.T., Telfer, S.J. and Waterman, S., In Roberts, S.M. (Ed.) Molecular Recognition: Chemical and Biological Problems. Royal Society of Chemistry, Cambridge, 1989, pp. 182-196.
41. Moock, T.E., Henry, D.R., Ozkabak, A.G. and Alamgir, M., J. Chem. Inf. Comput. Sci., 34 (1994) 184.
42. Thorner, D.A., Wild, D.J., Willett, P. and Wright, P.M., J. Chem. Inf. Comput. Sci., 36 (1996) 900.
43. Thorner, D.A., Willett, P., Wright, P.M. and Taylor, R., J. Comput.-Aided Mol. Design, 11 (1997) 163.
44. Wild, D.J. and Willett, P., J. Chem. Inf. Comput. Sci., 36 (1996) 159.
45. Hahn, M., J. Chem. Inf. Comput. Sci., 37 (1997) 80.
46. Hahn, M., J. Med. Chem., 38 (1995) 2080.
47. Wang, T. and Zhou, J., J. Chem. Inf. Comput. Sci., 38 (1998) 71.
48. Xu, J., J. Chem. Inf. Comput. Sci., 36 (1996) 25.
49. Rarey, M. and Dixon, J.S., J. Comput.-Aided Mol. Design, 12 (1998) 471.
50. Orengo, C., Curr. Opin. Struct. Biol., 4 (1994) 429.
51. Holm, L. and Sander, C., Proteins, 19 (1994) 165.
52. Godzik, A., Protein Sci., 5 (1996) 1325.
53. Lattman, E.E. (Ed.) Critical Assessment of Techniques for Protein Structure Prediction (CASP2). Supplement 1 to Proteins: Structure, Function, and Genetics, 1997. See also http://PredictionCenter.llnl.gov/casp3/Casp3.html.
54. Gibrat, J.-F., Madej, T. and Bryant, S.H., Curr. Opin. Struct. Biol., 6 (1996) 377.
55. Holm, L. and Sander, C., J. Mol. Biol., 233 (1994) 123.
56. Taylor, W.R. and Orengo, C.A., J. Mol. Biol., 208 (1989) 1.
57. Fischer, D., Wolfson, H., Lin, S.L. and Nussinov, R., Protein Sci., 3 (1994) 769.
58. Alesker, V., Nussinov, R. and Wolfson, H.J., Protein Eng., 9 (1996) 1103.
59. Norel, R., Lin, S.L., Wolfson, H.L. and Nussinov, R., J. Mol. Biol., 252 (1995) 263.
60. Sandak, B., Nussinov, R. and Wolfson, H.J., Comput. Appl. Biosci., 11 (1995) 87.
61. Rarey, M., Wefing, S. and Lengauer, T., J. Comput.-Aided Mol. Design, 10 (1996) 41.
62. Rarey, M., Kramer, B., Lengauer, T. and Klebe, G., J. Mol. Biol., 261 (1996) 470.
63. Diederichs, K., Proteins, 23 (1995) 187.
64. Katchalski-Katzir, E., Shariv, I., Eisenstein, M., Friesem, A.A., Aflalo, C. and Vakser, I.A., Proc. Natl. Acad. Sci. USA, 89 (1992) 2195.
65. Lattman, E.E., Acta Crystallogr., B28 (1972) 1065.
66. May, A.C.W. and Johnson, M.S., Protein Eng., 8 (1995) 873.
67. May, A.C.W. and Johnson, M.S., Protein Eng., 7 (1994) 475.
68. Fredman, M.L., Bull. Math. Biol., 46 (1984) 553.
69. Poirrette, A.R., Artymiuk, P.J., Rice, D.W. and Willett, P., J. Comput.-Aided Mol. Design, 11 (1997) 557.
70. Connolly, M.L., J. Appl. Crystallogr., 16 (1983) 548.
71. Wallace, A.C., Borkakoti, N. and Thornton, J.M., Protein Sci., 6 (1997) 2308.
72. Escalier, V., Pothier, J., Soldano, H. and Viari, A., J. Comput. Biol., 5 (1998) 41.
73. Klebe, G., In Kubinyi, H. (Ed.) 3D QSAR in Drug Design. Theory, Methods and Applications. ESCOM, Leiden, 1993, pp. 173-199.
74. Bures, M.G., In Charifson, P.S. (Ed.) Practical Application of Computer-Aided Drug Design. Marcel Dekker, New York, NY, 1997, pp. 39-72.
75. Good, A.C., Hodgkin, E.E. and Richards, W.G., J. Chem. Inf. Comput. Sci., 32 (1992) 188.
76. Good, A.C., J. Mol. Graph., 10 (1992) 144.
77. Feuilleaubois, E., Fabart, V. and Douchet, P., SAR QSAR Env. Res., 1 (1993) 97.
78. Petitjean, M., J. Comput. Chem., 16 (1995) 80.
79. Grant, J.A., Gallardo, M.A. and Pickup, B.T., J. Comput. Chem., 17 (1996) 1653.
80. Grant, J.A. and Pickup, B.T., J. Phys. Chem., 99 (1995) 3503.
81. Cossé-Barbi, A. and Raji, M., J. Comput. Chem., 18 (1997) 1875.
82. McMahon, A.J. and King, P.M., J. Comput. Chem., 18 (1997) 151.
83. Nissink, J.W.M., Verdonk, M.L., Kroon, J., Mietzner, T. and Klebe, G., J. Comput. Chem., 18 (1997) 638.
84. Crowther, R.A., In Rossmann, M.G. (Ed.) The Molecular Replacement Method. Gordon & Breach, New York, NY, 1972, pp. 174-178.
85. Parretti, M.F., Kroemer, R.T., Rothman, J.H. and Richards, W.G., J. Comput. Chem., 18 (1997) 1344.
86. Lemmen, C., Hiller, C. and Lengauer, T., J. Comput.-Aided Mol. Design, 12 (1998) 491.
87. Klebe, G., Mietzner, T. and Weber, F., J. Comput.-Aided Mol. Design, 8 (1994) 751.
88. Lemmen, C. and Lengauer, T., J. Comput.-Aided Mol. Design, 11 (1997) 357.
89. Martin, Y.C., Tetrahedron Comput. Methodol., 3 (1990) 15.
90. Takahashi, Y., Maeda, S. and Sasaki, S.-I., Ann. Chimica Acta, 200 (1987) 363.
91. Masek, B.B., Merchant, A. and Matthew, J.B., J. Med. Chem., 36 (1993) 1230.
92. Sanz, F., Manaut, F., Rodríguez, J., Lozoya, E. and López-de-Briñas, E., J. Comput.-Aided Mol. Design, 7 (1993) 337.
93. Sanz, F., Manaut, F., Sanchez, J.A. and Lozoya, E., J. Mol. Struct., 230 (1991) 437.
94. Jain, A.N., Dietterich, T.G., Laterop, R.H., Chapman, D., Critchlow, R.E., Bauer, B.E., Webster, T.A. and Lonzano-Perez, T., J. Comput.-Aided Mol. Design, 8 (1994) 427.
95. Jain, A.N., Koile, K. and Chapman, D., J. Med. Chem., 37 (1994) 2315.
96. Ghuloum, A.M., Sage, C.R. and Jain, A.J., J. Med. Chem., 42 (1999) 1739.
97. Ruppert, J., Welch, W. and Jain, A.N., Protein Sci., 6 (1997) 524.
98. Welch, W., Ruppert, J. and Jain, A.N., Chem. Biol., 3 (1996) 449.
99. Jain, A.N., J. Comput.-Aided Mol. Design, 10 (1996) 635.
100. Gerber, P.R. and Müller, K., Acta Crystallogr., A43 (1987) 426.
101. Klebe, G., Mietzner, T. and Weber, F., J. Comput.-Aided Mol. Design, 13 (1999), 35.
102. Waszkowycz, B., Clark, D.E., Frenkel, D., Li, J., Murray, C.W., Robson, B. and Westhead, D.R., J. Med. Chem., 37 (1994) 3994.
103. Cramer, R.D., Patterson, D.E. and Bunce, J.D., J. Am. Chem. Soc., 110 (1988) 5959.
104. Clark, D.E., Frenkel, D., Levy, S.A., Li, J., Murray, C.W., Robson, B., Waszkowycz, B. and Westhead, D.R., J. Comput-Aided Mol. Design, 9 (1995) 13.
105. Perkins, T.D.J., Mills, J.E.J. and Dean, P.M., J. Comput.-Aided Mol. Design, 9 (1995) 479.
106. Barakat, M.T. and Dean, P.M., J. Comput.-Aided Mol. Design, 5 (1991) 107.
107. Danziger, D.J. and Dean, P.M., J. Theor. Biol., 116 (1985) 215.
108. Perkins, T.D.J. and Dean, P.M., J. Comput.-Aided Mol. Design, 7 (1993) 155.
109. Barnum, D., Greene, J., Smellie, A. and Sprague, P., J. Chem. Inf. Comput. Sci., 36 (1996) 563.
110. Smellie, A., Teig, S.L. and Towbin, P., J. Comput. Chem., 16 (1995) 171.
111. Ferro, D.R. and Hermans, J., Acta Crystallogr., A33 (1977) 345.
112. Sprague, P.W., Perspect. Drug Discov. Design, 3 (1995) 21.
113. Finn, P.W., Kavraki, L., Latombe, J.-C., Motwani, R., Shelton, C., Venkatasubramanian, S. and Yao, A., Proceedings of the 13th Annual Symposium on Computational Geometry, ACM Press, New York, NY, 1997.
114. Finn, P.W., Halperin, D., Kavraki, L., Latombe, J.-C., Motwani, R., Shelton, C. and Venkatasubramanian, S., In Lin, M. and Manocha, D. (Eds) 1996 ACM Workshop on Applied Computational Geometry, LNCS, Springer-Verlag, Heidelberg, 1996.
115. Mestres, J., Rohrer, D.C. and Maggiora, G.M., J. Mol. Graphics Mod., 15 (1997) 114.
116. Mestres, J., Rohrer, D.C. and Maggiora, G.M., J. Comput. Chem., 18 (1997) 934.
117. Miller, M.D., Sheridan, R.P. and Kearsley, S.K., J. Med. Chem., 42 (1999) 1505.
118. Sheridan, R.P., Miller, M.D., Underwood, D.J. and Kearsley, S.K., J. Chem. Inf. Comput. Sci., 36 (1996) 128.
119. Kearsley, S.K., Smith, G.M., Sallamack, S., Fluder, E.M., Andose, J.D., Mosley, R.T. and Sheridan, R.P., J. Chem. Inf. Comput. Sci., 36 (1996) 118.
120. Kearsley, S.K., Underwood, D.J., Sheridan, R.P. and Miller, M.D., J. Comput.-Aided Mol. Design, 8 (1994) 565.
121. Sheridan, R.P., Nilakantan, R., Dixon, J.S. and Venkataraghavan, R., J. Med. Chem., 29 (1986) 899.
122. Crippen, G.M., J. Med. Chem., 22 (1979) 988.
123. Crippen, G.M., J. Med. Chem., 23 (1980) 599.
124. Crippen, G.M., J. Med. Chem., 24 (1981) 198.
125. Crippen, G.M., Smellie, A.S. and Richardson, W.W., J. Comput. Chem., 13 (1992) 1262.
126. Billeter, M., Havel, T.F. and Kuntz, I.D., Biopolymers, 26 (1987) 777.
127. Clark, D.E., Willett, P. and Kenny, P.W., J. Mol. Graph., 11 (1993) 146.
128. Sheridan, R.P. and Venkataraghavan, R., J. Comput.-Aided Mol. Design, 1 (1987) 243.
129. Sheridan, R.P., Rusinko III, A., Nilakantan, R. and Venkataraghavan, R., Proc. Natl. Acad. Sci. USA, 86 (1989) 8125.
130. Itai, A., Tomioka, N., Yamada, M., Inoue, A. and Kato, Y., In Kubinyi, H. (Ed.) 3D QSAR in Drug Design. Theory, Methods and Applications. ESCOM, Leiden, 1993, pp. 173-199.
131. Dammkoehler, R.A., Karasek, S.F., Shands, E.F.B. and Marshall, G.R., J. Comput.-Aided Mol. Design, 9 (1995) 491.
132. Marshall, G.R., Barry, C.D., Bosshard, H.D., Dammkoehler, R.D. and Dunn, D.A., In Olson, E.C. and Christoffersen, R.E. (Eds) Computer-Assisted Drug Design. Vol. 112. American Chemical Society, Washington, DC, 1979, pp. 205-222.
133. Ghose, A.K., Logan, M.E., Treasuywala, A.M., Wang, H., Wahl, R.C., Tomczuk, B.E., Gowravaram, M.R., Jaeger, E.P. and Wendoloski, J.J., J. Am. Chem. Soc., 117 (1995) 4671.
134. McMartin, C. and Bohacek, R.S., J. Comput.-Aided Mol. Design, 9 (1995) 237.
135. Chang, G., Guida, W.C. and Still, W.C., J. Am. Chem. Soc., 111 (1989) 4379.
136. Jones, G., Willett, P. and Glen, R.C., J. Comput.-Aided Mol. Design, 9 (1995) 532.
137. Jones, G., Willett, P. and Glen, R.C., J. Mol. Biol., 245 (1995) 43.
138. Payne, A.W.R. and Glen, R.C., J. Mol. Graph., 11 (1993) 74.
139. Pepperrell, C.A. and Willett, P., J. Comput.-Aided Mol. Design, 5 (1991) 455.
140. Lemmen, C., Lengauer, T. and Klebe, G., J. Med. Chem., 41 (1998) 4502.
141. Handschuh, S., Wagener, M. and Gasteiger, J., J. Chem. Inf. Comput. Sci., 38 (1998) 220.
142. Kato, Y., Inoue, A., Yamada, M., Tomioka, N. and Itai, A., J. Comput.-Aided Mol. Design, 6 (1992) 475.