Challenges for Computer Simulations in Drug Design

Challenges and Advances in Computational Chemistry and Physics

Volumn 12, Issue , 2010, Pages 431-463

  Wallnoefer, Hannes G ^a,b   Fox, Thomas ^a   Liedl, Klaus R ^b  

^a BOEHRINGER INGELHEIM PHARMA GMBH AND CO KG   (Germany)

^b UNIVERSITY OF INNSBRUCK   (Austria)

Author keywords

Docking; FEP TI; Flexibility; Free energy prediction; GPCR simulations; Linear interaction energy; MM GBSA; MM PBSA; Molecular dynamics; Pharmacophore modelling; Simulations; Structure based drug design; Virtual screening; Water in proteins

Indexed keywords

EID: 79953738878     PISSN: 25424491     EISSN: 25424483     Source Type: Book Series    
DOI: 10.1007/978-90-481-3034-4_16     Document Type: Chapter

References (324)

1. Greer J, Erickson JW, Baldwin JJ et al (2002) J Med Chem 37:1035–1054
2. Jorgensen WL (2004) Science 303:1813–1818
3. Chand P, Kotian PL, Dehghani A et al (2001) J Med Chem 44:4379–4392
4. Gubernator K, Böhm H-J (1998) structure-based ligand design. Wiley-VCH Verlag GmbH, Weinheim
5. Hazuda DJ, Anthony NJ, Gomez RP et al (2004) Proc Natl Acad Sci USA 101:11233–11238
6. Schames JR, Henchman RH, Siegel JS et al (2004) J Med Chem 47:1879–1881
7. Liverton NJ, Holloway MK, McCauley JA et al (2008) J Am Chem Soc 130:4607–4609
8. Thomson JA, Perni RB (2006) Curr Opin Drug Disc Dev 9:606–617
9. Stauffer SR, Stanton MG, Gregro AR et al (2007) Bioorg Med Chem Lett 17:1788–1792
10. Hop CECA, Cole MJ, Davidson RE et al (2008) Curr Drug Metab 9:847–853
11. Jamei M, Marciniak S, Feng KR et al (2009) Expert Opin Drug Metab Toxicol 5:211–223
12. Nogueira RC, Oliveira-Costa JF, De Sa MS et al (2009) Curr Drug Targets 10:291–298
13. Selick HE, Beresford AP, Tarbit MH (2002) Drug Disc Today 7:109–116
14. van de Waterbeemd H, Gifford E (2003) Nat Drug Disc 2:192–204
15. Wang J, Hou T (2009) Annu Rep Comput Chem 5:101–103
16. Bolton V, Perutz M (1970) Nature 228:551–552
17. Fermi G, Perutz M, Shaanan B et al (1984) J Mol Biol 175:159–174
18. Kendrew J, Bodo GR, Dintzis H et al (1958) Nature 181:662–666
19. Watson H (1969) Prog Stereochem 4:299–333
20. Safo MK, Abraham DJ (2005) Biochemistry 44:8347–8359
21. Wolf-Watz M, Thai V, Henzler-Wildman K et al (2004) Nat Struct Mol Biol 11:945–949
22. Vonrhein C, Schlauderer GJ, Schulz GE (2009) Structure 3:483–490
23. Henzler-Wildman KA, Lei M, Thai V et al (2007) Nature 450:913–916
24. Hu X, Lazar MA (2000) Trends Endocrinol Metab 11:6–10
25. Hellal-Levy C, Fagart J, Souque A et al (2000) Mol Endocrinol 14:1210–1221
26. Henzler-Wildman K, Kern D (2007) Nature 450:964–972
27. Bahar I, Chennubhotla C, Tobi D (2007) Curr Opin Struct Biol 17:633–640
28. Cozzini P, Kellogg GE, Spyrakis F et al (2008) J Med Chem 51:6237–6255
29. Lee GM, Craik CS (2009) Science 324:213–215
30. Tsai CJ, Ma B, Nussinov R (1999) Proc Natl Acad Sci USA 96:9970–9972
31. Koshland DE, Nemethy G, Filmer D (2002) Biochemistry 5:365–385
32. Monod J, Wyman J, Changeux JP (1965) J Mol Biol 12:88–118
33. Weber G (2002) Biochemistry 11:864–878
34. Tsai CJ, Kumar S, Ma B et al (1999) Protein Sci 8:1181–1190
35. Berman HM, Westbrook J, Feng Z et al (2000) Nucl Acid Res 28:235–242
36. Tompa P (2002) Trends Biochem Sci 27:527–533
37. Zheng Q, Kyle DJ (1997) Drug Disc Today 2:229–234
38. Walters WP, Stahl MT, Murcko MA (1998) Drug Disc Today 3:160–178
39. Ma B, Kumar S, Tsai CJ et al (1999) Protein Eng 12:713–720
40. Freire E (1998) In: Richards FM (ed) Advances in protein chemistry – linkage thermodynamics of macromolecular interactions. Academic, San Diego, CA
41. Onuchic JN (1997) Proc Natl Acad Sci USA 94:7129–7131
42. Shoemaker B, Wang J, Wolynes P (1997) Proc Natl Acad Sci USA 94:777–782
43. Rejto PA, Freer ST (1996) Prog Biophys Mol Biol 66:167–196
44. Brem R, Dill KA (1999) Protein Sci 8:1134–1143
45. Boehr DD, Dyson HJ, Wright PE (2006) Chem Rev 106:3055–3079
46. Wuthrich K (2003) J Biomol NMR 27:13–39
47. Mulder FAA, Mittermaier A, Hon B et al (2001) Nat Struct Mol Biol 8:932–935
48. Ishima R, Torchia DA (2000) Nat Struct Mol Biol 7:740–743
49. Eisenmesser EZ, Millet O, Labeikovsky W et al (2005) Nature 438:117–121
50. Horst R, Wider G, Fiaux J et al (2006) Proc Natl Acad Sci USA 103:15445–15450
51. Grishaev A, Tugarinov V, Kay L et al (2008) J Biomol NMR 40:95–106
52. Sprangers R, Velyvis A, Kay LE (2007) Nat Meth 4:697–703
53. Liang B, Tamm LK (2007) Proc Natl Acad Sci USA 104:16140–16145
54. Cioffi M, Hunter CA, Packer MJ et al (2008) J Med Chem 51:2512–2517
55. Ramos CRR, Figueredo RCR, Pertinhez TA et al (2003) J Biol Chem 278:12745–12751
56. Pertinhez T, Sforça M, Alves A et al (2004) J Biomol NMR 29:553–554
57. Vitkup D, Ringe D, Karplus M et al (2002) Proteins 46:345–354
58. Merritt E (1999) Acta Cryst Sect D 55:1109–1117
59. Schmidt A, Lamzin V (2007) Cell Mol Life Sci 64:1959–1969
60. Bossi RT, Aliverti A, Raimondi D et al (2002) Biochemistry 41:8807–8818
61. Ringe D, Petsko GA (1985) Prog Biophys Mol Biol 45:197–235
62. Bourgeois D, Royant A (2005) Curr Opin Struct Biol 15:538–547
63. Somogyi B, Lakos Z, Szarka A et al (2000) J Photochem Photobiol B: Biol 59:26–32
64. Hubbell WL, Cafiso DS, Altenbach C (2000) Nat Struct Mol Biol 7:735–739
65. Lipfert J, Doniach S (2007) Annu Rev Biophys Biomol Struct 36:307–327
66. Katona G, Carpentier P, Niviere V et al (2007) Science 316:449–453
67. McCammon JA, Gelin BR, Karplus M (1977) Nature 267:585–590
68. Freddolino PL, Liu F, Gruebele M et al (2008) Biophys J 94:L75–L77
69. Klepeis JL, Lindorff-Larsen K, Dror RO et al (2009) Curr Opin Struct Biol 19:120–127
70. Maragakis P, Lindorff-Larsen K, Eastwood MP et al (2008) J Phys Chem B 112:6155–6158
71. Perez A, Luque FJ, Orozco M (2007) J Am Chem Soc 129:14739–14745
72. Romo TD, Grossfield A, Pitman MC et al (2009) Biophys J 96:340a–340a
73. Vaiana AC, Sanbonmatsu KY (2009) J Mol Biol 386:648–661
74. McCammon JA, Wolynes PG, Karplus M (2002) Biochemistry 18:927–942
75. van Gunsteren WF, Karplus M (1981) Nature 293:677–678
76. Lin H, Truhlar DG (2007) Theor Chem Acc 117:185–199
77. Gleeson MP, Gleeson D (2009) J Chem Inf Model 49:1437–1448
78. Senn HM, Thiel W (2009) Angew Chem Int Ed 48:1198–1229
79. Bakowies D, Thiel W (1996) J Phys Chem 100:10580–10594
80. Gogonea V, Subrez D, Avd V et al (2001) Curr Opin Struct Biol 11:217–223
81. Case DA, Darden TE, Cheatham TE et al (2008) AMBER 10. University of California, San Francisco, CA
82. Brooks BR, Bruccoleri RE, Olafson BD et al (1983) J Comput Chem 4:187–217
83. Van Der Spoel D, Lindahl E, Hess B et al (2005) J Comput Chem 26:1701–1718
84. Phillips JC, Braun R, Wang W et al (2005) J Comput Chem 26:1781–1802
85. Berendsen HJC, Postma J, van Gunsteren W et al (1981) In: Pullman B (ed) Intermolecular Forces. D.Reidel, Dordrecht, The Nederlands
86. Jorgensen WL, Maxwell DS, Tirado-Rives J (1996) J Am Chem Soc 118:11225–11236
87. Mongan J (2004) J Comput Aided Mol Des 18:433–436
88. Hess B (2000) Phys Rev E 62:8438
89. Hess B (2002) Phys Rev E 65:031910
90. Gund P (1977) Prog Mol Subcell Biol 5:117–143
91. Mallik B, Morikis D (2005) J Am Chem Soc 127:10967–10976
92. Bernard D, Coop A, MacKerell AD (2003) J Am Chem Soc 125:3101–3107
93. Deng J, Taheri L, Grande F et al (2008) Chem Med Chem 3:1677–1686
94. Meagher KL, Carlson HA (2004) J Am Chem Soc 126:13276–13281
95. Meagher KL, Lerner MG, Carlson HA (2006) J Med Chem 49:3478–3484
96. Carlson HA, Masukawa KM, Rubins K et al (2000) J Med Chem 43:2100–2114
97. Deng J, Sanchez T, Neamati N et al (2006) J Med Chem 49:1684–1692
98. Bowman AL, Lerner MG, Carlson HA (2007) J Am Chem Soc 129:3634–3640
99. Damm KL, Carlson HA (2007) J Am Chem Soc 129:8225–8235
100. Kuntz ID, Blaney JM, Oatley SJ et al (1982) J Mol Biol 161:269–288
101. Goodsell DS, Olson AJ (1990) Proteins 8:195–202
102. Morris GM, Goodsell DS, Huey R et al (1996) J Comput Aided Mol Des 10:293–304
103. Morris GM, Goodsell DS, Halliday RS et al (1998) J Comput Chem 19:1639–1662
104. Rarey M, Kramer B, Lengauer T et al (1996) J Mol Biol 261:470–489
105. Cavasotto CN, Abagyan RA (2004) J Mol Biol 337:209–225
106. Claussen H, Buning C, Rarey M et al (2001) J Mol Biol 308:377–395
107. Huey R, Morris GM, Olson AJ et al (2007) J Comput Chem 28:1145–1152
108. Jain A (2007) J Comput Aided Mol Des 21:281–306
109. Österberg F, Morris GM, Sanner MF et al (2002) Proteins 46:34–40
110. Verdonk ML, Cole JC, Hartshorn MJ et al (2003) Proteins 52:609–623
111. Wei BQ, Weaver LH, Ferrari AM et al (2004) J Mol Biol 337:1161–1182
112. Jones G, Willett P, Glen RC (1995) J Mol Biol 245:43–53
113. Schnecke V, Swanson CA, Getzoff ED et al (1998) Proteins 33:74–87
114. Leach AR (1994) J Mol Biol 235:345–356
115. Schaffer L, Verkhivker GM (1998) Proteins 33:295–310
116. Zavodszky MI, Kuhn LA (2005) Protein Sci 14:1104–1114
117. Zavodszky MI, Lei M, Thorpe MF et al (2004) Proteins 57:243–261
118. Cavasotto CN, Kovacs JA, Abagyan RA (2005) J Am Chem Soc 127:9632–9640
119. Kallblad P, Dean PM (2003) J Mol Biol 326:1651–1665
120. Nabuurs SB, Wagener M, de Vlieg J (2007) J Med Chem 50:6507–6518
121. Kuhn LA (2008) In: Stroud RM, Finer-Moore J (eds) Computational and structural approaches to drug discovery: ligand-protein interactions. RSC Publishing, Cambridge
122. McCammon JA (2005) Biochim Biophys Acta 1754:221–224
123. Lin JH, Perryman AL, Schames JR et al (2002) J Am Chem Soc 124:5632–5633
124. Lin J-H, Perryman AL, Schames JR et al (2003) Biopolymers 68:47–62
125. Knegtel RMA, Kuntz ID, Oshiro CM (1997) J Mol Biol 266:424–440
126. Macchiarulo A, Nobeli I, Thornton JM (2004) Nat Biotech 22:1039–1045
127. Sotriffer CA, Dramburg I (2005) J Med Chem 48:3122–3125
128. Klebe G, Kramer O, Sotriffer CA (2004) Cell Mol Life Sci 61:783–793
129. Sotriffer CA, Kramer O, Klebe G (2004) Proteins 56:52–66
130. Steuber H, Zentgraf M, Gerlach C et al (2006) J Mol Biol 363:174–187
131. Steuber H, Zentgraf M, Podjarny A et al (2006) J Mol Biol 356:45–56
132. Da Settimo F, Primofiore G, La Motta C et al (2005) J Med Chem 48:6897–6907
133. Zentgraf M, Steuber H, Koch C et al (2007) Angew Chem Int Ed 46:3575–3578
134. Hamelberg D, Mongan J, McCammon JA (2004) J Chem Phys 120:11919–11929
135. Egbertson MS (2007) Curr Top Med Chem 7:1251–1272
136. Keskin O, Gursoy A, Ma B et al (2008) Chem Rev 108:1225–1244
137. Król M, Tournier AL, Bates PA (2007) Proteins 68:159–169
138. Gottschalk KE, Neuvirth H, Schreiber G (2004) Protein Eng 17:183–189
139. Duan Y, Reddy BVB, Kaznessis YN (2005) Protein Sci 14:316–328
140. Smith GR, Sternberg MJE, Bates PA (2005) J Mol Biol 347:1077–1101
141. Burlingham BT, Widlanski TS (2003) J Chem Educ 80:214–218
142. Yung-Chi C, Prusoff WH (1973) Biochem Pharmacol 22:3099–3108
143. Cheluvaraja S, Meirovitch H (2008) J Chem Theor Comput 4:192–208
144. Cheluvaraja S, Mihailescu M, Meirovitch H (2008) J Phys Chem B 112:9512–9522
145. Deng Y, Roux B (2009) J Phys Chem B 113:2234–2246
146. Meirovitch H, Cheluvaraja S, White RP (2009) Curr Protein Pept Sci 10:229–243
147. Mihailescu M, Meirovitch H (2009) J Phys Chem B 113:7950–7964
148. Miyamoto S, Kollman PA (1993) Proteins 16:226–245
149. Zhang X, Mamonov AB, Zuckerman DM (2009) J Comput Chem 30:1680–1691
150. Kirkwood JG (1935) J Chem Phys 3:300–313
151. Zwanzig RW (1954) I Nonpolar Gases J Chem Phys 22:1420–1426
152. Åqvist J, Medina C, Samuelsson JE (1994) Protein Eng 7:385–391
153. Lee MS, Olson MA (2006) Biophys J 90:864–877
154. Kollman P (1993) Chem Rev 93:2395–2417
155. Huang N, Jacobson MP (2007) Curr Opin Drug Disc Dev 10:325–331
156. Gilson MK, Zhou HX (2007) Annu Rev Biophys Biomol Struct 36:21
157. Foloppe N, Hubbard RE (2006) Curr Med Chem 13:3583–3608
158. Honig B, Nicholls A (1995) Science 268:1144–1149
159. Still WC, Tempczyk A, Hawley RC et al (1990) J Am Chem Soc 112:6127–6129
160. Bryce RA, Hillier IH, Naismith JH (2001) Biophys J 81:1373–1388
161. Bashford D, Case DA (2000) Annu Rev Phys Chem 51:129–152
162. Kuhn B, Kollman PA (2000) J Med Chem 43:3786–3791
163. Gouda H, Kuntz ID, Case DA et al (2003) Biopolymers 68:16–34
164. Barril X, Gelpi JL, Lopez JM et al (2001) Theor Chem Acc 106:2–9
165. Masukawa KM, Kollman PA, Kuntz ID (2003) J Med Chem 46:5628–5637
166. Bea I, Cervello E, Kollman PA et al (2001) Comb Chem High Throughput Screen 4:605–611
167. Cox SR, Williams DE (1981) J Comput Chem 2:304–323
168. Pearlman DA (2005) J Med Chem 48:7796–7807
169. Swanson JMJ, Henchman RH, McCammon JA (2004) Biophys J 86:67–74
170. Gilson MK, Honig B (1988) Proteins 4:7–18
171. Scarsi M, Caflisch A (1999) J Comput Chem 20:1533–1536
172. Sharp KA (1994) Curr Opin Struct Biol 4:234–239
173. Holst M, Saied F (1993) J Comput Chem 14:105–113
174. Warwicker J, Watson HC (1982) J Mol Biol 157:671–679
175. Honig B, Nicholls A (1995) Science 268:1144–1149
176. Gilson MK, Sharp KA, Honig BH (1988) J Comput Chem 9:327–335
177. Shen J, Wendoloski J (1996) J Comput Chem 17:350–357
178. Baker NA, Sept D, Joseph S et al (2001) Proc Natl Acad Sci USA 98:10037–10041
179. Bashford D, Gerwert K (1992) J Mol Biol 224:473–486
180. Im W, Beglov D, Roux B (1998) Comput Phys Commun 111:59–75
181. Ma C, Baker NA, Joseph S et al (2002) J Am Chem Soc 124:1438–1442
182. Madura JD, Briggs JM, Wade RC et al (1995) Comput Phys Commun 91:57–95
183. Gilson MK, Honig BH (1986) Biopolymers 25:2097–2119
184. Sharp KA, Honig B (1990) Annu Rev Biophys Biophys Chem 19:301–332
185. Simonson T, Perahia D (1995) Proc Natl Acad Sci USA 92:1082–1086
186. Simonson T, Perahia D (1995) Comput Phys Commun 91:291–303
187. Antosiewicz J, McCammon JA, Gilson MK (1994) J Mol Biol 238:415–436
188. Demchuk E, Wade RC (1996) J Phys Chem 100:17373–17387
189. Demchuk E, Genick UK, Woo TT et al (2000) Biochemistry 39:1100–1113
190. Foloppe N, Sagemark J, Nordstrand K et al (2001) J Mol Biol 310:449–470
191. Grant JA, Pickup BT, Nicholls A (2001) J Comput Chem 22:608–640
192. Richards FM (1977) Annu Rev Biophys Bioeng 6:151–176
193. Swanson JMJ, Mongan J, McCammon JA (2005) J Phys Chem B 109:14769–14772
194. Nina M, Beglov D, Roux B (1997) J Phys Chem B 101:5239–5248
195. Nina M, Im W, Roux B (1999) Biophys Chem 78:89–96
196. Sitkoff D, Sharp KA, Honig B (1994) J Phys Chem 98:1978–1988
197. Swanson JMJ, Adcock SA, McCammon JA (2005) J Chem Theory Comput 1:484–493
198. Wang J, Morin P, Wang W et al (2001) J Am Chem Soc 123:5221–5230
199. Froloff N, Windemuth A, Honig B (1997) Protein Sci 6:1293–1301
200. Huo S, Wang J, Cieplak P et al (2002) J Med Chem 45:1412–1419
201. Schwarzl SM, Tschopp TB, Smith JC et al (2002) J Comput Chem 23:1143–1149
202. Tanford C (1978) Science 200:1012–1018
203. Blokzijl W, Engberts JBFN (1993) Angew Chem Int Ed 32:1545–1579
204. Gao J, Qiao S, Whitesides GM (1995) J Med Chem 38:2292–2301
205. Hunenberger PH, Helms V, Narayana N et al (1999) Biochemistry 38:2358–2366
206. Janin J, Chothia C (1978) Biochemistry 17:2943–2948
207. Scarsi M, Majeux N, Caflisch A (1999) Proteins 37:565–575
208. Hermann RB (1972) J Phys Chem 76:2754–2759
209. Reynolds JA, Gilbert DB, Tanford C (1974) Proc Natl Acad Sci USA 71:2925–2927
210. Sims PA, Wong CF, McCammon JA (2003) J Med Chem 46:3314–3325
211. Shen J, Wendoloski J (1995) Protein Sci 4:373–381
212. Sharp KA, Nicholls A, Fine RF et al (1991) Science 252:106–109
213. Doyle ML (1997) Curr Opin Biotechnol 8:31–35
214. Leavitt S, Freire E (2001) Curr Opin Struct Biol 11:560–566
215. Weber PC, Salemme FR (2003) Curr Opin Struct Biol 13:115–121
216. Finkelstein AV, Janin J (1989) Protein Eng 3:1–3
217. Murray CW, Verdonk ML (2002) J Comput Aided Mol Des 16:741–753
218. Page MI, Jencks WP (1971) Proc Natl Acad Sci USA 68:1678–1683
219. Gidofalvi G, Wong CF, McCammon JA (2002) J Chem Educ 79:1122–1126
220. Sirockin F, Sich C, Improta S et al (2002) J Am Chem Soc 124:11073–11084
221. Searle MS, Williams DH (1992) J Am Chem Soc 114:10690–10697
222. Bonnet P, Bryce RA (2004) Protein Sci 13:946–957
223. Foloppe N, Fisher LM, Howes R et al (2005) J Med Chem 48:4332–4345
224. Steinbrecher T, Case DA, Labahn A (2006) J Med Chem 49:1837–1844
225. Zhou Z, Madura JD (2004) Proteins 57:493–503
226. Kollman PA, Massova I, Reyes C et al (2000) Acc Chem Res 33:889–897
227. Hou T, Guo S, Xu X (2002) J Phys Chem B 106:5527–5535
228. Karplus M, Kushick JN (1981) Macromolecules 14:325–332
229. Ferrara P, Gohlke H, Price DJ et al (2004) J Med Chem 47:3032–3047
230. Huang D, Caflisch A (2004) J Med Chem 47:5791–5797
231. Kuhn B, Gerber P, Schulz-Gasch T et al (2005) J Med Chem 48:4040–4048
232. Zou X, Sun Y, Kuntz ID (1999) J Am Chem Soc 121:8033–8043
233. Barril X, Aleman C, Orozco M et al (1998) Proteins 32:67–79
234. Woods CJ, King MA, Essex JW (2001) J Comput Aided Mol Des 15:129–144
235. Rizzo RC, Toba S, Kuntz ID (2004) J Med Chem 47:3065–3074
236. Donini OAT, Kollman PA (2000) J Med Chem 43:4180–4188
237. Kuhn B, Kollman PA (2000) J Med Chem 43:3786–3791
238. Mardis KL, Luo R, Gilson MK (2001) J Mol Biol 309:507–517
239. Zhou R, Friesner RA, Ghosh A et al (2001) J Phys Chem B 105:10388–10397
240. Resat H, McCammon JA (1996) J Chem Phys 104:7645–7651
241. Simonson T, Archontis G, Karplus M (2002) Acc Chem Res 35:430–437
242. Åqvist J (1996) J Comput Chem 17:1587–1597
243. Åqvist J, Marelius J (2001) Comb Chem High Throughput Screen 4:613–626
244. Åqvist J, Luzhkov VB, Brandsdal BO (2002) Acc Chem Res 35:358–365
245. Jones-Hertzog DK, Jorgensen WL (1997) J Med Chem 40:1539–1549
246. Hansson T, Marelius J, Åqvist J (1998) J Comput Aided Mol Des 12:27–35
247. Essex JW, Jorgensen WL (1995) J Comput Chem 16:951–972
248. Pierce AC, Jorgensen WL (2001) J Med Chem 44:1043–1050
249. Wall ID, Leach AR, Salt DW et al (1999) J Med Chem 42:5142–5152
250. Wang J, Dixon R, Kollman PA (1999) Proteins 34:69–81
251. Zoete V, Michielin O, Karplus M (2003) J Comput Aided Mol Des 17:861–880
252. Ljungberg KB, Marelius J, Musil D et al (2001) Eur J Pharm Sci 12:441–446
253. Hansson T, Åqvist J (1995) Protein Eng 8:1137–1144
254. Tounge BA, Reynolds CH (2003) J Med Chem 46:2074–2082
255. Rizzo RC, Tirado-Rives J, Jorgensen WL (2001) J Med Chem 44:145–154
256. Svab I, Alexandru D, Vitos G et al (2004) J Cell Mol Med 8:551–562
257. Dey I (1999) J Biomol Struct Dyn 16:891–900
258. Lamb ML, Tirado-Rives J, Jorgensen WL (1999) Bioorg Med Chem 7:851–860
259. Smith RH Jr, Jorgensen WL, Tirado-Rives J et al (1998) J Med Chem 41:5272–5286
260. Pierce KL, Premont RT, Lefkowitz RJ (2002) Nat Rev Mol Cell Biol 3:639–650
261. Hulten J, Bonham NM, Nillroth U et al (1997) J Med Chem 40:885–897
262. Graffner-Nordberg M, Kolmodin K, Åqvist J et al (2001) J Med Chem 44:2391–2402
263. Singh P, Mhaka AM, Christensen SB et al (2005) J Med Chem 48:3005–3014
264. Paulsen MD, Ornstein RL (1996) Protein Eng 9:567–571
265. Chen J, Wang R, Taussig M et al (2001) J Org Chem 66:3021–3026
266. Wang W, Wang J, Kollman PA (1999) Proteins 34:395–402
267. Chipot C (2003) J Comput Chem 24:409–415
268. Carlson HA, Jorgensen WL (1995) J Phys Chem 99:10667–10673
269. Rizzo RC, Udier-Blagovic M, Wang DP et al (2002) J Med Chem 45:2970–2987
270. Jorgensen WL, Ravimohan C (1985) J Chem Phys 83:3050–3054
271. Jorgensen WL, Tirado-Rives J (2005) Proc Natl Acad Sci USA 102:6665–6670
272. Bennett CH (1976) J Comput Phys 22:245–268
273. Lawrenz M, Baron R, McCammon JA (2009) J Chem Theor Comput 5:1106–1116
274. Adcock SA, McCammon JA (2006) Chem Rev 106:1589–1615
275. Zagrovic B, van Gunsteren WF (2006) J Chem Theor Comput 3:301–311
276. Fujitani H, Tanida Y, Ito M et al (2005) J Chem Phys 123:084108–5
277. Reinhardt WP, Miller MA, Amon LM (2001) Acc Chem Res 34:607–614
278. Fajer M, Hamelberg D, McCammon JA (2008) J Chem Theor Comput 4:1565–1569
279. Woods CJ, Essex JW, King MA (2003) J Phys Chem B 107:13703–13710
280. de Oliveira CA, Hamelberg D, McCammon JA (2008) J Chem Theor Comput 4:1516–1525
281. Hamelberg D, de Oliveira CA, McCammon JA (2007) J Chem Phys 127:155102–155109
282. Steinbrecher T, Hrenn A, Dormann KL et al (2008) Bioorg Med Chem 16:2385–2390
283. Lundstrom K (2006) Curr Protein Pept Sci 7:465–470
284. Palczewski K (2006) Annu Rev Biochem 75:743
285. Fanelli F, De Benedetti PG (2005) Chem Rev 105:3297–3351
286. Cherezov V, Rosenbaum DM, Hanson MA et al (2007) Science 318:1258–1265
287. Rasmussen SGF, Choi HJ, Rosenbaum DM et al (2007) Nature 450:383–387
288. Warne T, Serrano-Vega MJ, Baker JG et al (2008) Nature 454:486–491
289. Kenakin T (2002) Nat Rev Drug Discov 1:103–110
290. Cremades N, Sancho J, Freire E (2006) Trends Biochem Sci 31:494–496
291. Barnett-Norris J, Lynch D, Reggio PH (2005) Life Sci 77:1625–1639
292. Fanelli F, De Benedetti PG (2006) J Comput Aided Mol Des 20:449–461
293. Feng X, Muller T, Mizrachi D et al (2008) Endocrinol 149:1705–1717
294. Angelova K, Fanelli F, Puett D (2008) Mol Endocrinol 22:126–138
295. Raimondi F, Seeber M, De Benedetti PG et al (2008) J Am Chem Soc 130:4310–4325
296. Seeber M, De Benedetti PG, Fanelli F (2003) J Chem Inf Model 43:1520–1531
297. Vitale RM, Pedone C, De Benedetti PG et al (2004) Proteins 56:430–448
298. Yan F, Mosier PD, Westkaemper RB et al (2008) Biochemistry 47:1567–1578
299. Ballesteros JA, Jensen AD, Liapakis G et al (2001) J Biol Chem 276:29171–29177
300. Dror RO, Arlow DH, Borhani DW et al (2009) Proc Natl Acad Sci USA 106:4689–4694
301. Wolf S, Böckmann M, Höweler U et al (2008) FEBS lett 582:3335–3342
302. Hamelberg D, McCammon JA (2004) J Am Chem Soc 126:7683–7689
303. Lu YP, Yang CY, Wang SM (2006) J Am Chem Soc 128:11830–11839
304. Zhang L, Hermans J (1996) Proteins 24:433–438
305. Olano LR, Rick SW (2004) J Am Chem Soc 126:7991–8000
306. Lounnas V, Pettitt BM (1994) Proteins 18:133–147
307. Bizzarri AR, Cannistraro S (2002) J Phys Chem B 106:6617–6633
308. Luise A, Falconi M, Desideri A (2000) Proteins 39:56–67
309. Otting G, Liepinsh E, Wuthrich K (1991) Science 254:974–980
310. Henchman RH, McCammon JA (2002) J Comput Chem 23:861–869
311. Huang HC, Jupiter D, Qiu M et al (2008) Biopolymers 89:210–219
312. Brunne RM, Liepinsh E, Otting G et al (1993) J Mol Biol 231:1040–1048
313. Barillari C, Taylor J, Viner R et al (2007) J Am Chem Soc 129:2577–2587
314. Abel R, Young T, Farid R et al (2008) J Am Chem Soc 130:2817–2831
315. Lazaridis T (1998) The Journal of Physical Chemistry B 102:3531–3541
316. Van Drie J (2007) J Comput Aided Mol Des 21:591–601
317. Moore GE (1965) Electronics 38:114–117
318. Mitsutake A, Sugita Y, Okamoto Y (2001) Biopolymers 60:86–123
319. Okabe T, Kawata M, Okamoto Y et al (2001) Chem Phys Lett 335:435–439
320. Berg BA, Neuhaus T (1992) Phys RevLett 68:9–12
321. Kubitzki MB, de Groot BL (2007) Biophys J 92:4262–4270
322. Shaw, DE, Deneroff, MM, Dror, RO et al (2007) Anton, a special-purpose machine for molecular dynamics simulation. Proceedings of the 34th annual international symposium on computer architecture, San Diego, California
323. Miller BT, Singh RP, Klauda JB et al (2008) J Chem Inf Model 48:1920–1929
324. Stjernschantz E, Marelius J, Medina C et al (2006) J Chem Inf Model 46:1972–1983