Comparative Protein Structure Modeling and its Applications to Drug Discovery

Annual Reports in Medicinal Chemistry

Volumn 39, Issue , 2004, Pages 259-276

  Jacobson, Matthew ^a   Sali, Andrej ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 12844260161     PISSN: 00657743     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0065-7743(04)39020-2     Document Type: Review

References (147)

1. Brenner S.E. Nat. Struct. Biol 7 (2000) 967
2. Boeckmann B., Bairoch A., Apweiler R., Blatter M.C., Estreicher A., Gasteiger E., Martin M.J., Michoud K., O'Donovan C., Phan I., et al. Nuclic Acids Res 31 (2003) 365
3. Benson D.A., Karsch-Mizrachi I., Lipman D.J., Ostell J., Rapp B.A., and Wheeler L. Nucleic Acids Res 30 (2002) 17
4. Berman H.M., Battistuz T., Bhat T.N., Bluhm W.F., Bourne P.E., Burkhardt K., Feng Z., Gilliland G.L., Iype L., Jain S., et al. Acta Crystallogr. D 58 (2002) 899
5. Baker D., and Sali A. Science 294 (2001) 93
6. Marti-Renom M.A., Stuart A., Fiser A., Sanchez R., Melo F., and Sali A. Annu. Rev. Biophys. Biomol. Struct 29 (2000) 291
7. Bonneau R., and Baker D. Annu. Rev. Biophys. Biomol. Struct 30 (2001) 173
8. Baker D. Nature 405 (2000) 39
9. Pieper U., Eswar N., Braberg H., Madhusudhan M.S., Davis F.P., Stuart A.C., Mirkovic N., Rossi A., Marti-Renom M.A., Fiser A., et al. Nucleic Acids Res 32 (2004) D217. http://www.salilab.org/modbase/ Database issue, http://www.salilab.org/modbase/ and http://www.nysqxrc.org/
10. Fischer D., Elofsson A., Rychlewski L., Pazos F., Valencia A., Rost B., Ortiz A.R., and Dunbrack Jr. R.L. Proteins 45 Suppl. 5 (2001) 171
11. Bourne P.E. Methods Biochem. Anal 44 (2003) 501
12. Bujnicki J.M., Elofsson A., Fischer D., and Rychlewski L. Prot. Sci 10 (2001) 352
13. Eyrich V.A., Marti-Renom M.A., Przybylski D., Madhusudhan M.S., Fiser A., Pazos F., Valencia A., Sali A., and Rost B. Bioinformatics 17 (2001) 1242
14. Koh I.-Y.Y., Eyrich V.A., Marti-Renom M.A., Przybylski D., Madhusudhan M.S., Narayanan E., Graca O., Pazos F., Valencia A., Sali A., et al. Nucleic Acids Res (2003)
15. Sali A. Nat. Struct. Biol 5 (1998) 1029
16. Burley S.K., Almo S.C., Bonanno J.B., Capel M., Chance M.R., Gaasterland T., Lin D., Sali A., Studier F.W., and Swaminathan S. Nat. Genet 23 (1999) 151
17. Vitkup D., Melamud E., Moult J., and Sander C. Nat. Struct. Biol 8 (2001) 559
18. Altschul S.F., Gish W., Miller W., Myers E.W., and Lipman D.J. J. Mol. Biol 215 (1990) 403
19. Pearson W.R. Methods Enzymol 183 (1990) 63
20. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., and Lipman D.J. Nucleic Acids Res 25 (1997) 3389
21. Marti-Renom M.A., Madhusudhan M.S., and Sali A. Prot. Sci 13 (2004) 1071
22. Karchin R., Cline M., Mandel-Gutfreund Y., and Karplus M. Proteins 51 (2003) 504
23. Torda A.E. Curr. Opin. Struct. Biol 7 (1997) 200
24. John B., and Sali A. Nucleic Acids Res 31 (2003) 3982-3992
25. Browne W.J., North A.C.T., Phillips D.C., Brew K., Vanaman T.C., and Hill R.C. J. Mol. Biol 42 (1969) 65
26. Greer J. J. Mol. Biol 153 (1981) 1027
27. Blundell T.L., Sibanda B.L., Sternberg M.J., and Thornton J.M. Nature 326 (1987) 347
28. Levitt M. J. Mol. Biol 226 (1992) 507
29. Havel T.F., and Snow M.E. J. Mol. Biol 217 (1991) 1
30. Sali A., and Blundell T.L. J. Mol. Biol 234 (1993) 779
31. Kolinski A., Betancourt M.R., Kihara D., Rotkiewicz P., and Skolnick J. Proteins 44 (2001) 133
32. Kabsch W., and Sander C. Proc. Natl. Acad. Sci. USA 81 (1984) 1075
33. Mezei M. Prot. Eng 11 (1998) 411
34. Fiser A., Do R.K., and Sali A. Prot. Sci 9 (2000) 1753. http://www.salilab.org http://www.salilab.org/modeller
35. Jacobson M.P., Pincus D.L., Rapp C.S., Day T.J., Honig B., Shaw D.E., and Friesner R.A. Proteins 55 (2004) 351
36. Jones T.A., and Thirup S. EMBO J 5 (1986) 819
37. Chothia C., and Lesk M. J. Mol. Biol 196 (1987) 901
38. Moult J., and James M.N. Proteins 1 (1986) 146
39. Bruccoleri R.E., and Karplus M. Biopolymers 26 (1987) 137
40. Shenkin P.S., Yarmush D.L., Fine R.M., Wang H.J., and Levinthal C. Biopolymers 26 (1987) 2053
41. van Vlijmen H.W., and Karplus M. J. Mol. Biol 267 (1997) 975
42. Deane C.M., and Blundell T.L. Prot. Sci 10 (2001) 599
43. Sibanda B.L., Blundell T.L., and Thornton J.M. J. Mol. Biol 206 (1989) 759
44. Chothia C., Lesk A.M., Tramontano A., Levitt M., Smith-Gill S.J., Air G., Sheriff S., Padlan E.A., Davies D., Tulip W.R., et al. Nature 342 (1989) 877
45. Ring C.S., Kneller D.G., Langridge R., and Cohen F.E. J. Mol. Biol 224 (1992) 685
46. Oliva B., Bates P.A., Querol E., Aviles F.X., and Sternberg M.J. J. Mol. Biol 266 (1997) 814
47. Rufino S.D., Donate L.E., Canard L.H., and Blundell T.L. J. Mol. Biol 267 (1997) 352
48. Fidelis K., Stern P.S., Bacon D., and Moult J. Prot. Eng 7 (1994) 953
49. Lessel U., and Schomburg D. Prot. Eng 7 (1994) 1175-1187
50. Claessens M., Van Cutsem E., Lasters I., and Wodak S. Prot. Eng 2 (1989) 335
51. Fine R.M., Wang H., Shenkin P.S., Yarmush D.L., and Levinthal C. Proteins 1 (1986) 342
52. Bruccoleri R.E., and Karplus M. Biopolymers 29 (1990) 1847
53. Ring C.S., Sun E., McKerrow J.H., Lee G.K., Rosenthal P.J., Kuntz I.D., and Cohen F.E. Proc. Natl Acad. Sci. USA 90 (1993) 3583
54. Higo J., Collura V., and Garnier J. Biopolymers 32 (1992) 33
55. Collura V., Higo J., and Garnier J. Prot. Sci 2 (1993) 1502
56. Abagyan R., and Totrov M. J. Mol. Biol 235 (1994) 983
57. Zheng Q., Rosenfeld R., Vajda S., and DeLisi C. Prot. Sci 2 (1993) 1242
58. Koehl P., and Delarue M. Nat. Struct. Biol 2 (1995) 163
59. Samudrala R., and Moult J. J. Mol. Biol 279 (1998) 287
60. Xiang Z., Soto C.S., and Honig B. Proc. Natl Acad. Sci. USA 99 (2002) 7432-7437
61. Felts A.K., Gallicchio E., Wallqvist A., and Levy R.M. Proteins 48 (2002) 404
62. de Bakker P.I., DePristo M.A., Burke D.F., and Blundell T.L. Proteins 51 (2003) 21
63. DePristo M.A., de Bakker P.I., Lovell S.C., and Blundell T.L. Proteins 51 (2003) 41
64. Jacobson M.P., Pincus D.L., Rapp C.S., Day T.J.F., Honig B., Shaw D.E., and Friesner R.A. Proteins 55 (2004) 351
65. Chothia C., Lesk A.M., Levitt M., Amit A.G., Mariuzza R.A., Phillips S.E., and Poljak R.J. Science 233 (1986) 755
66. Janin J., and Chothia C. Biochemistry 17 (1978) 2943
67. Ponder J.W., and Richards F.M. J. Mol. Biol 193 (1987) 775
68. Tuffery P., Etchebest C., Hazout S., and Lavery R. J. Biomol. Struct. Dyn 8 (1991) 1267
69. Dunbrack R.L., and Karplus M. J. Mol. Biol 230 (1993) 543
70. Dunbrack Jr. R.L., and Cohen F.E. Prot. Sci 6 (1997) 1661
71. Mendes J., Baptista A.M., Carrondo M.A., and Soares C.M. Proteins 37 (1999) 530
72. Xiang Z., and Honig B. J. Mol. Biol 311 (2001) 421-430
73. Desjarlais J.R., and Handel T.M. J. Mol. Biol 290 (1999) 305
74. De Filippis V., Sander C., and Vriend G. Prot. Eng 7 (1994) 1203
75. Chung S.Y., and Subbiah S. Pac. Symp. Biocomput (1996) 126
76. Cregut D., Liautard J.P., and Chiche L. Prot. Eng 7 (1994) 1333
77. Canutescu A.A., Shelenkov A.A., and Dunbrack Jr. R.L. Prot. Sci 12 (2003) 2001
78. Eisenmenger F., Argos P., and Abagyan R. J. Mol. Biol 231 (1993) 849
79. Lee G.M., Varma A., and Palsson B.O. Biotechnol. Prog 7 (1991) 72
80. Holm L., and Sander C. Proteins 14 (1992) 213
81. Lasters I., and Desmet J. Prot. Eng 6 (1993) 717
82. Looger L.L., and Hellinga H.W. J. Mol. Biol 307 (2001) 429
83. Hwang J.K., and Liao W.F. Prot. Eng 8 (1995) 363
84. Koehl P., and Delarue M. J. Mol. Biol 239 (1994) 249
85. Bower M.J., Cohen F.E., and Dunbrack Jr. R.L. J. Mol. Biol 267 (1997) 1268
86. Petrella R.J., Lazaridis T., and Karplus M. Fold. Des 3 (1998) 353
87. Jacobson M.P., Kaminski G.A., Friesner R.A., and Rapp C.S. J. Phys. Chem. B 106 (2002) 11673
88. Liang S., and Grishin N.V. Prot. Sci 11 (2002) 322
89. MacKerell Jr. A.D., Bashford D., Bellott M., Dunbrack Jr. R.L., Evanseck J.D., Field M.J., Fischer S., Gao J., Guo H., Ha S., et al. J. Phys. Chem. B 102 (1998) 3586
90. Sali A., and Overington J.P. Prot. Sci 3 (1994) 1582-1596
91. Rapp C.S., and Friesner R.A. Proteins 35 (1999) 173
92. Fiser A., Feig M., Brooks III C.L., and Sali A. Acc. Chem. Res 35 (2002) 413
93. Jacobson M.P., Friesner R.A., Xiang Z.X., and Honig B. J. Mol. Biol 320 (2002) 597
94. Hornak V., and Simmerling C. Proteins 51 (2003) 577
95. Moult J. Curr. Opin. Biotechnol 7 (1996) 422
96. Koehl P., and Levitt M. Nat. Struct. Biol 6 (1999) 108
97. Dominy B.N., and Brooks C.L. J. Comp. Chem 23 (2002) 147
98. Li H., Tejero R., Monleon D., BassolinoKlimas D., AbateShen C., Bruccoleri R.E., and Montelione G.T. Prot. Sci 6 (1997) 956
99. Flohil J.A., Vriend G., and Berendsen H.J.C. Proteins 48 (2002) 593
100. Jorgensen W.L., and Tiradorives J. J. Am. Chem. Soc 110 (1988) 1666
101. Kaminski G.A., Friesner R.A., Tirado-Rives J., and Jorgensen W.L. J. Phys. Chem. B 105 (2001) 6474
102. Ghosh A., Rapp C.S., and Friesner R.A. J. Phys. Chem. B 102 (1998) 10983
103. Gallicchio E., Zhang L.Y., and Levy R.M. J. Comp. Chem 23 (2002) 517
104. Li X., Jacobson M.P., and Friesner R.A. Proteins (2004)
105. Sanchez R., and Sali A. Proc. Natl Acad. Sci. USA 95 (1998) 13597
106. Marti-Renom M.A., Madhusudhan M.S., Fiser A., Rost B., and Sali A. Structure 10 (2002) 435
107. Fischer D., and Eisenberg D. Proc. Natl Acad. Sci. USA 94 (1997) 11929
108. Guex N., Diemand A., and Peitsch M.C. Trends Biochem. Sci 24 (1999) 364
109. Eswar N., John B., Mirkovic N., Fiser A., Ilyin V.A., Pieper U., Stuart A.C., Marti-Renom M.A., Madhusudhan M.S., Yerkovich B., et al. Nucleic Acids Res 31 (2003) 3375. http://www.salilab.org/modweb http://www.salilab.org/modweb
110. Huang C.C., Novak W.R., Babbitt P.C., Jewett A.I., Ferrin T.E., and Klein T.E. Pac. Symp. Biocomput (2000) 230
111. Marti-Renom M.A., Ilyin V.A., and Sali A. Bioinformatics 17 (2001) 746. http://www.salilab.org/dbali http://www.salilab.org/dbali
112. Fiser A., and Sali A. Bioinformatics 19 (2003) 2500
113. Mirkovic N., Marti-Renom M.A., Sali A., and Monteiro A.N.A. Cancer Res 64 (2004) 3790
114. Gordon R.K., Ginalski K., Rudnicki W.R., Rychlewski L., Pankaskie M.C., Bujnicki J.M., and Chiang P.K. Eur. J. Biochem 270 (2003) 3507
115. von Grotthuss M., Wyrwicz L.S., and Rychlewski L. Cell 113 (2003) 701
116. Schafferhans A., and Klebe G. J. Mol. Biol 307 (2001) 407-427
117. Evers A., Gohlke H., and Klebe G. J. Mol. Biol 334 (2003) 327-345
118. Evers A., and Klebe G. Angew Chem. Int. Ed. Engl 43 (2004) 248-251
119. McGovern S.L., and Shoichet B.K. J. Med. Chem 46 (2003) 2895
120. Li R., Chen X., Gong B., Selzer P.M., Li Z., Davidson E., Kurzban G., Miller R.E., Nuzum E.O., McKerrow J.H., et al. Bioorg. Med. Chem. Lett 4 (1996) 1421
121. Selzer P.M., Chen X., Chan V.J., Cheng M., Kenyon G.L., Kuntz I.D., Sakanari J.A., Cohen F.E., and McKerrow J.H. Exp. Parasitol 87 (1997) 212
122. Que X., Brinen L.S., Perkins P., Herdman S., Hirata K., Torian B.E., Rubin H., McKerrow J.H., and Reed S.L. Mol. Biochem. Parasitol 119 (2002) 23
123. Enyedy I.J., Lee S.L., Kuo A.H., Dickson R.B., Lin C.Y., and Wang S. J. Med. Chem 44 (2001) 1349
124. Enyedy I.J., Ling Y., Nacro K., Tomita Y., Wu X., Cao Y., Guo R., Li B., Zhu X., Huang Y., et al. J. Med. Chem 44 (2001) 4313
125. Schapira M., Raaka B.M., Samuels H.H., and Abagyan R. BMC Struct. Biol 1 (2001) 1
126. Zuccotto F., Zvelebil M., Brun R., Chowdhury S.F., Di Lucrezia R., Leal I., Maes L., Ruiz-Perez L.M., Gonzalez Pacanowska D., and Gilbert I.H. Eur. J. Med. Chem 36 (2001)
127. Vriend G. J. Mol. Graph 8 (1990) 52
128. Diller D.J., and Li R. J. Med. Chem 46 (2003) 4638
129. Diller D.J., and Merz K.M. Proteins 43 (2001) 113
130. Oshiro C., Bradley E.K., Eksterowicz J., Evensen E., Lamb M.L., Lanctot J.K., Putta S., Stanton R., and Grootenhuis P.D. J. Med. Chem 47 (2004) 764
131. Rockey W.M., and Elcock A.H. Proteins 48 (2002) 664
132. Bissantz C., Bernard P., Hibert M., and Rognan D. Proteins 50 (2003) 5
133. Cavasotto C.N., Orry A.J., and Abagyan R.A. Proteins 51 (2003) 423
134. Vaidehi N., Floriano W.B., Trabanino R., Hall S.E., Freddolino P., Choi E.J., Zamanakos G., and Goddard III W.A. Proc. Natl Acad. Sci. USA 99 (2002) 12622
135. Shacham S., Topf M., Avisar N., Glaser F., Marantz Y., Bar-Haim S., Noiman S., Naor Z., and Becker O.M. Med. Res. Rev 21 (2001) 472
136. Becker O.M., Shacham S., Marantz Y., and Noiman S. Curr. Opin. Drug. Discov. Devel 6 (2003) 353
137. Sabnis Y.A., Desai P.V., Rosenthal P.J., and Avery M.A. Prot. Sci 12 (2003) 501
138. Price M.L., Guida W.C., Jackson T.E., Nydick J.A., Gladstone P.L., Juarez J.C., Donate F., and Ternansky R.J. Bioorg. Med. Chem. Lett 13 (2003) 107
139. Spadola L., Novellino E., Folkers G., and Scapozza L. Eur. J. Med. Chem 38 (2003) 413
140. Marhefka C.A., Moore B.M., Bishop II T.C., Kirkovsky L., Mukherjee A., Dalton J.T., and Miller D.D. J. Med. Chem 44 (2001) 1729
141. Rabinowitz M.H., Andrews R.C., Becherer J.D., Bickett D.M., Bubacz D.G., Conway J.G., Cowan D.J., Gaul M., Glennon K., Lambert M.H., et al. J. Med. Chem 44 (2001) 4252
142. Delfino R.T., Santos-Filho O.A., and Figueroa-Villar J.D. Biophys. Chem 98 (2002) 287
143. Salter E.A., Wierzbicki A., Sperl G., and Thompson W.J. Int. J. Quantum Chem 96 (2004) 402
144. Vangrevelinghe E., Zimmermann K., Schoepfer J., Portmann R., Fabbro D., and Furet P. J. Med. Chem 46 (2003) 2656
145. Honma T., Hayashi K., Aoyama T., Hashimoto N., Machida T., Fukasawa K., Iwama T., Ikeura C., Ikuta M., Suzuki-Takahashi I., Iwasawa Y., Hayama T., Nishimura S., and Morishima H. J. Med. Chem 44 (2001) 4628
146. http://www.francisco.compbio.ucsf.edu/~jacobson/plop_overview.htm.
147. http://www.salilab.org/bioinformatics_resources.shtml.