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Extending the horizon: towards the efficient modeling of large biomolecular complexes in atomic detail

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Abstract

The application of evaluation of implicit solvent methods for the simulation of biomolecules is described. Detailed comparisons with explicit solvent are described for the modeling of peptide and proteins in continuum aqueous solvent. In addition, we are presenting new data on the simulation of DNA with implicit solvent and describe the development of a heterogeneous dielectric model for the simulation of integral membranes. The performance of implicit solvent simulations based on the GBMV generalized Born method is compared with explicit solvent simulations, and implications for the simulation of very large biomolecular complexes is discussed. We are anticipating that the work described herein will lead to new, efficient modeling tools that will allow the simulation of longer timescales and larger system sizes in order to meet current and future challenges by the experimental community.

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References

  1. York DM, Yang W, Lee H, Darden TA, Pedersen L (1995) J Am Chem Soc 117:5001–5002

    Article  CAS  Google Scholar 

  2. Smith PE, Pettitt BM (1995). Comput Phys Commun 91:339–344

    Article  CAS  Google Scholar 

  3. Luty BA, Davis ME, Tironi IG, Gunsteren WF (1994). Mol Simul 14:11

    CAS  Google Scholar 

  4. Cheatham TE, Miller JL, Fox T, Darden TA, Kollman PA (1995). J Am Chem Soc 117:4193–4194

    Article  CAS  Google Scholar 

  5. Straub JE, Whitfield T, Andricioaei I (2002). Abstr Pap Am Chem Soc 223:U470–U470

    Google Scholar 

  6. Okamoto Y (2004). J Mol Graph Model 22:425–439

    PubMed  CAS  Google Scholar 

  7. Hansmann UHE (1997). Chem Phys Lett 281:140–150

    Article  CAS  Google Scholar 

  8. Hornak V, Simmerling C (2004). J Mol Graph Model 22:405–413

    Article  PubMed  CAS  Google Scholar 

  9. Micheletti C, Laio A, Parrinello M (2004). Phys Rev Lett 92:170601

    Article  PubMed  CAS  Google Scholar 

  10. MacKerell AD Jr, Feig M, Brooks CL III (2004). J Comput Chem 25:1400–1415

    PubMed  CAS  Google Scholar 

  11. MacKerell AD Jr, Feig M, Brooks CL III (2004). J Am Chem Soc 126:698–699

    Article  PubMed  CAS  Google Scholar 

  12. Feig M, MacKerell AD Jr, Brooks CL III (2003). J Phys Chem B 107:2831–2836

    Article  CAS  Google Scholar 

  13. Patel S, Brooks CL (2004). J Comput Chem 25:1–15

    Article  PubMed  CAS  Google Scholar 

  14. MacKerell AD Jr, Banavali NK, Foloppe N (2001). Biopolymers 56:257–265

    Article  Google Scholar 

  15. Oostenbrink C, Villa A, Mark AE, Van Gunsteren WF (2004). J Comput Chem 25:1656–1676

    PubMed  CAS  Google Scholar 

  16. Mackerell AD (2004). J Comput Chem 25:1584–1604

    Article  PubMed  CAS  Google Scholar 

  17. Patel S, Mackerell AD, Brooks CL (2004). J Comput Chem 25:1504–1514

    Article  PubMed  CAS  Google Scholar 

  18. Patel S, Brooks CL (2005). J Chem Phys 122:24508

    Article  CAS  Google Scholar 

  19. Wang JM, Wolf RM, Caldwell JW, Kollman PA, Case DA (2004). J Comput Chem 25:1157–1174

    Article  PubMed  CAS  Google Scholar 

  20. Gao J, Truhlar DG (2002). Annu Rev Phys Chem 53:267–505

    Article  CAS  Google Scholar 

  21. Li GH, Cui Q (2003). J Phys Chem B 107:14521–14528

    Article  CAS  Google Scholar 

  22. Svensson M, Humbel S, Froese RDJ, Matsubara T, Sieber S, Morokuma K (1996). J Phys Chem 100:19357–19363

    Article  CAS  Google Scholar 

  23. Gnanakaran S, Nymeyer H, Portman J, Sanbonmatsu K Y, Garcia AE (2003). Curr Opin Struct Biol 13:168–174

    Article  PubMed  CAS  Google Scholar 

  24. Pande VS, Rokhsar DS (1996). Proc Nat Acad Sci USA 96:9062–9067

    Article  Google Scholar 

  25. Mayor U, Johnson CM, Daggett V, Fersht AR (2000). Proc Nat Acad Sci USA 97:13518–13522

    Article  PubMed  CAS  Google Scholar 

  26. Bozcko EM, Brooks CL III (1995). Science 269:393–396

    PubMed  Google Scholar 

  27. Pitera JW, Swope WC (2003). Proc Nat Acad Sci USA 100:7587–7592

    Article  PubMed  CAS  Google Scholar 

  28. Simmerling C, Strockbine B, Roitberg AE (2002). J Am Chem Soc 124:11258–11259

    Article  PubMed  CAS  Google Scholar 

  29. Okur A, Roe DR, Cui GL, Hornak V, Simmerling C (2003). Abstr Pap Am Chem Soc 226:U450–U451

    Google Scholar 

  30. Zagrovic B, Sorin E, Pande V (2002). Biophys J 82:474a–474a

    Google Scholar 

  31. Brooks CL (2002). Acc Chem Res 35:447–454

    Article  PubMed  CAS  Google Scholar 

  32. Brooks CL (1998). Curr Opin Struct Biol 8:222–226

    Article  PubMed  CAS  Google Scholar 

  33. Andricioaei I, Goel A, Herschbach D, Karplus M (2004). Biophys J 87:1478–1497

    Article  PubMed  CAS  Google Scholar 

  34. Florian J, Goodman MF, Warshel A (2003). Biopolymers 68:286–299

    Article  PubMed  CAS  Google Scholar 

  35. Rittenhouse RC, Apostoluk WK, Miller JH, Straatsma TP (2003). Proteins Struct Funct Genet 53:667–682

    Article  PubMed  CAS  Google Scholar 

  36. Sanbonmatsu KY, Joseph S (2003). J Mol Biol 328:33–47

    Article  PubMed  CAS  Google Scholar 

  37. Trylska J, Konecny R, Tama F, Brooks CL, McCammon JA (2004). Biopolymers 74:423–431

    Article  PubMed  CAS  Google Scholar 

  38. Ramakrishnan V, Moore PB (2001). Curr Opin Struct Biol 11:144–154

    Article  PubMed  CAS  Google Scholar 

  39. Ban N, Nissen P, Hansen J, Moore PB, Steitz TA (2000). Science 289:905–920

    Article  PubMed  CAS  Google Scholar 

  40. Westover KD, Bushnell DA, Kornberg RD (2004). Science 303:1014–1016

    Article  CAS  Google Scholar 

  41. Bushnell DA, Kornberg RD (2003). Proc Nat Acad Sci USA 100:6969–6973

    Article  PubMed  CAS  Google Scholar 

  42. Gnatt AL, Cramer P, Fu JH, Bushnell DA, Kornberg RD (2001). Science 292:1876–1882

    Article  PubMed  CAS  Google Scholar 

  43. Cramer P, Bushnell DA, Kornberg RD (2001). Science 292:1863–1876

    Article  PubMed  CAS  Google Scholar 

  44. Zhirnov VV, Cavin RK III, Hutchby JA, Bourianoff GI (2003). Proc IEEE 91:1934–1939

    Article  Google Scholar 

  45. Schlick T, Barth E, Mandziuk M (1997). Ann Rev Biophys Biomol Struct 26:179–220

    Google Scholar 

  46. Zhou RH, Harder E, Xu HF, Berne BJ (2001). J Chem Phys 115:2348–2358

    Article  CAS  Google Scholar 

  47. Barth E, Schlick T (1998). J Chem Phys 109:1633–1642

    Article  CAS  Google Scholar 

  48. Gront D, Kolinski A, Skolnick J (2001). J Chem Phys 115:1569–1574

    Article  CAS  Google Scholar 

  49. Rao F, Caflisch A (2003). J Chem Phys 119:4035–4042

    Article  CAS  Google Scholar 

  50. Rhee YM, Pande VS (2003). Biophys J 84:775–786

    PubMed  CAS  Google Scholar 

  51. Sanbonmatsu KY, Garcia AE (2002). Proteins 46:225–234

    Article  PubMed  CAS  Google Scholar 

  52. Sugita Y, Okamoto Y (1999). Chem Phys Lett 314:141–151

    Article  CAS  Google Scholar 

  53. Suenaga A (2003). J Mol Struct (Theochem). 634:235–241

    Article  CAS  Google Scholar 

  54. Zhou R, Berne BJ, Germain R (2001). Proc Nat Acad Sci USA 98:14931–14936

    Article  PubMed  CAS  Google Scholar 

  55. Garcia AE, Sanbonmatsu KY (2002). Proc Nat Acad Sci USA 99:2782–2787

    Article  PubMed  CAS  Google Scholar 

  56. Garcia AE, Sanbonmatsu KY (2001). Proteins 42:345–354

    Article  PubMed  CAS  Google Scholar 

  57. Beutler TC, Gunsteren WF (1993). J Chem Phys 100:1492–1497

    Article  Google Scholar 

  58. Fraternali F, Gunsteren WF (1994). Biopolymers 34:347–355

    Article  CAS  Google Scholar 

  59. Schmidt RK, Teo B, Brady JW (1995). J Phys Chem 99:11339–11343

    Article  CAS  Google Scholar 

  60. Torrie GM, Valleau JP (1974). Chem Phys Lett 28:578–581

    Article  CAS  Google Scholar 

  61. Hansmann UHE, Okamoto Y (1999). Curr Opin Struct Biol 9:177–183

    Article  PubMed  CAS  Google Scholar 

  62. Nakajima N, Nakamura H, Kidera A (1997). J Phys Chem 101:817–824

    Article  CAS  Google Scholar 

  63. Lin C-Y, Hu C-K, Hansmann UHE (2003). Proteins 52:436–445

    Article  PubMed  CAS  Google Scholar 

  64. Hansmann UHE (2002). Comput Phys Commun 147:604–607

    Article  CAS  Google Scholar 

  65. Guo ZY, Thirumalai D, Honeycutt JD (1992). J Chem Phys 97:525–535

    Article  CAS  Google Scholar 

  66. Camacho CJ, Thirumalai D (1993). Proc Nat Acad Sci USA 90:6369–6372

    PubMed  CAS  Google Scholar 

  67. Dill KA (1985). Biochemistry 24:1501–1509

    Article  PubMed  CAS  Google Scholar 

  68. Dill KA, Fiebig KM, Chan HS (1993). Proc Nat Acad Sci USA 90:1942–1946

    PubMed  CAS  Google Scholar 

  69. Dill KA, Chan HS, Sun SJ, Yue K (1995). Faseb J 9:A1240–A1240

    Google Scholar 

  70. Yue K, Fiebig KM, Thomas PD, Chan HS, Shakhnovich EI, Dill KA (1995). Proceedings of the National Academy of Sciences of the United States of America 92:325–329

    PubMed  CAS  Google Scholar 

  71. Kolinski A, Skolnick J, Yaris R (1986). Proc Nat Acad Sci USA 83:7267–7271

    PubMed  CAS  Google Scholar 

  72. Liwo A, Oldziej S, Pincus MR, Wawak RJ, Rackovsky S, Scheraga HA (1997). J Comput Chem 18:849–873

    Article  CAS  Google Scholar 

  73. Liwo A, Pincus MR, Wawak RJ, Rackovsky S, Oldziej S, Scheraga HA (1997). J Comput Chem 18:874–887

    Article  CAS  Google Scholar 

  74. Kolinski A (2004). Acta Biochimica Pol 51:349–371

    CAS  Google Scholar 

  75. Kolinski A, Skolnick J (1994). Proteins 18:338–352

    Article  PubMed  CAS  Google Scholar 

  76. Skolnick J, Kolinski A, Ortiz AR (1997). J Mol Biol 265:217–241

    Article  PubMed  CAS  Google Scholar 

  77. Hinds DA, Levitt M (1992). Proc Nat Acad Sci USA 89:2536–2540

    PubMed  CAS  Google Scholar 

  78. Malhotra A, Tan RK-Z, Harvey SC (1994). Biophyisics J 66:1777–1795

    CAS  Google Scholar 

  79. Langowski J, Olson WK, Yang Y (1996). Trends Biochem Sci 21:50

    Article  PubMed  CAS  Google Scholar 

  80. Fenley MO, Olson WK, Tobias I, Manning GS (1994). Biophys Chem 50:255–271

    Article  PubMed  CAS  Google Scholar 

  81. Feig M, Rotkiewicz P, Kolinski A, Skolnick J, Brooks CLI (2000). Proteins 41:86–97

    Article  PubMed  CAS  Google Scholar 

  82. Milik M, Kolinski A, Skolnick J (1997). J Comput Chem 18:80–85

    Article  CAS  Google Scholar 

  83. Payne PW (1993). Protein Sci 2:315–324

    Article  PubMed  CAS  Google Scholar 

  84. Rey A, Skolnick J (1992). J Comput Chem 13:443–456

    Article  CAS  Google Scholar 

  85. Feig M, Karanicolas J, Brooks CL III (2004). J Mol Graph Model 22:377–395

    Article  PubMed  CAS  Google Scholar 

  86. Feig M, Brooks CL III (2004). Curr Opin Struct Biol 14:217–224

    Article  PubMed  CAS  Google Scholar 

  87. Cramer CJ, Truhlar DG (1999). Chem Rev 99:2161–2200

    Article  PubMed  CAS  Google Scholar 

  88. Lazaridis T, Karplus M (2000). Curr Opin Struct Biol 10:139–145

    Article  PubMed  CAS  Google Scholar 

  89. Hao M-H, Scheraga HA (1999). Curr Opin Struct Biol 9:184–188

    Article  PubMed  CAS  Google Scholar 

  90. Hou T, Qiao X, Zhang W, Xu X (2002). J Phys Chem B 106:11295–11304

    Article  CAS  Google Scholar 

  91. Wesson L, Eisenberg D (1992). Protein Sci 1:227–235

    Article  PubMed  CAS  Google Scholar 

  92. Zhou H, Zhou Y (2002). Proteins 49:483–492

    Article  PubMed  CAS  Google Scholar 

  93. Ferrara P, Apostolakis J, Caflish A (2002). Proteins 46:24–33

    Article  PubMed  CAS  Google Scholar 

  94. Ooi T, Obatake M, Nemethy G, Scheraga HA (1987). Proc Nat Acad Sci USA 84

    Google Scholar 

  95. Mallik B, Masunov A, Lazaridis T (2002). J Comput Chem 23:1090–1099

    Article  PubMed  CAS  Google Scholar 

  96. Lazaridis T, Karplus M (1999). Proteins 35:133–152

    Article  PubMed  CAS  Google Scholar 

  97. Lazaridis T (2003). Proteins 52:176–192

    PubMed  CAS  Google Scholar 

  98. Lazaridis T, Karplus M (1998). J Mol Biol 288:477–487

    Article  Google Scholar 

  99. Forrest LR, Woolf TB (2003). Proteins 52:492–509

    PubMed  CAS  Google Scholar 

  100. Feig M, Brooks CL III (2002). Proteins 49:232–245

    PubMed  CAS  Google Scholar 

  101. Sitkoff D, Sharp KA, Honig B (1994). J Phys Chem 98:1978–1988

    Article  CAS  Google Scholar 

  102. Hassan SA, Mehler EL (2002). Proteins 47:45–61

    PubMed  CAS  Google Scholar 

  103. Sharp KA, Honig B (1990). Ann Rev Biophys Biophys Chem 19:301–332

    Article  CAS  Google Scholar 

  104. Luque FJ, Alhambra C, Orozco M (1995). J Phys Chem 99:11344–11349

    Article  CAS  Google Scholar 

  105. Hecht JL, Honig B, Shin YK, Hubbell WL (1995). J Phys Chem 99:7782–7786

    Article  CAS  Google Scholar 

  106. Misra VK, Honig B (1996). Biochemistry 35:1115–1124

    PubMed  CAS  Google Scholar 

  107. Srinivasan J, Miller J, Kollman PA, Case DA (1998). J Biomol Struct Dyn 16:671–682

    PubMed  CAS  Google Scholar 

  108. Srinivasan J, Cheatham TE, Cieplak P, Kollman P A, Case DA (1998). J Am Chem Soc 120:9401–9409

    Article  CAS  Google Scholar 

  109. Levy RM, Zhang LY, Gallicchio E, Felts AK (2003). J Am Chem Soc 125:9523–9530

    PubMed  CAS  Google Scholar 

  110. Gallicchio E, Levy RM (2004). J Comput Chem 25:479–499

    PubMed  CAS  Google Scholar 

  111. Hawkins GD, Cramer CJ, Truhlar DG (1996). J Phys Chem 100:19824–19839

    Article  CAS  Google Scholar 

  112. Floris F, Tomasi J (1989). J Comput Chem 10:616–627

    CAS  Google Scholar 

  113. Felts AK, Gallicchio E, Wallqvist A, Levy RM (2002). Proteins 48:404–422

    PubMed  CAS  Google Scholar 

  114. Lee MR, Duan Y, Kollman PA (2000). Proteins 39:309–316

    PubMed  CAS  Google Scholar 

  115. Lee MR, Kollman PA (2001). Structure 9:905–916

    Article  PubMed  CAS  Google Scholar 

  116. Dominy BN, Brooks CL III (2001). J Comput Chem 23:147–160

    Article  Google Scholar 

  117. Rapp CS, Friesner RA (1999). Proteins 35:173–183

    Article  PubMed  CAS  Google Scholar 

  118. Lee MC, Duan Y (2004). Proteins 55:620–634

    Article  PubMed  CAS  Google Scholar 

  119. Gohlke H, Kiel C, Case DA (2003). J Mol Biol 330:891–913

    Article  PubMed  CAS  Google Scholar 

  120. Gohlke H, Case DA (2003). J Comput Chem 25:238–250

    Article  CAS  Google Scholar 

  121. Mardis KL, Luo R, Gilson MK (2001). J Mol Biol 309:507–517

    Article  PubMed  CAS  Google Scholar 

  122. Zhang LY, Gallicchio E, Friesner RA, Levy RM (2001). J Comput Chem 22:591–607

    Article  CAS  Google Scholar 

  123. Zhou R, Friesner RA, Ghosh A, Rizzo RC, Jorgensen WL, Levy RM (2001). J Phys Chem B 105:10388–10397

    Article  CAS  Google Scholar 

  124. Wang JM, Morin P, Wang W, Kollman PA (2001). J Am Chem Soc 123:5221–5230

    Article  PubMed  CAS  Google Scholar 

  125. Jang S, Shin S, Pak Y (2002). J Am Chem Soc 124:4976–4977

    Article  PubMed  CAS  Google Scholar 

  126. Krol M (2003). J Comput Chem 24:531–546

    Article  PubMed  CAS  Google Scholar 

  127. Zagrovic B, Sorin EJ, Pande V (2001). J Mol Biol 313:151–169

    Article  PubMed  CAS  Google Scholar 

  128. Luo R, David L, Gilson MK (2002). J Comput Chem 23:1244–1253

    PubMed  CAS  Google Scholar 

  129. Zhou R (2003). Proteins 53:148–161

    PubMed  CAS  Google Scholar 

  130. Nymeyer H, Garcia AE (2003). Proc Nat Acad Sci USA 100:13934–13939

    PubMed  CAS  Google Scholar 

  131. Feig M, Onufriev A, Lee MS, Im W, Case DA, Brooks CL III (2004). J Comput Chem 25:265–284

    PubMed  CAS  Google Scholar 

  132. Bashford D, Case DA (2000). Annu Rev Phys Chem 51:129–152

    PubMed  CAS  Google Scholar 

  133. Still WC, Tempczyk A, Hawley RC, Hendrickson T (1990). J Am Chem Soc 112:6127–6129

    Article  CAS  Google Scholar 

  134. Born M (1920). Zeitschrift für Physik 1:45–48

    Article  CAS  Google Scholar 

  135. Constanciel R, Contreras R (1984). Theor Chim Acta 65:1–11

    CAS  Google Scholar 

  136. Onufriev A, Case DA, Bashford D (2002). J Comput Chem 23:1297–1304

    PubMed  CAS  Google Scholar 

  137. Hawkins GD, Cramer CJ, Truhlar DG (1995). Chem Phys Lett 246:122–129

    Article  CAS  Google Scholar 

  138. Qiu D, Shenkin PS, Hollinger FP, Still WC (1997). J Phys Chem A 101:3005–3014

    Article  CAS  Google Scholar 

  139. Schaefer M, Karplus M (1996). J Phys Chem 100:1578–1599

    Article  CAS  Google Scholar 

  140. Lee MS, Salsbury FR Jr, Brooks CL III (2002). J Chem Phys 116:10606–10614

    Article  CAS  Google Scholar 

  141. Liotard DA, Hawkins GD, Lynch GC, Cramer CJ, Truhlar DG (1995). J Comput Chem 16:422–440

    Article  CAS  Google Scholar 

  142. Ghosh A, Rapp CS, Friesner RA (1998). J Phys Chem B 102:10983–10990

    Article  CAS  Google Scholar 

  143. Feig M, Im W, Brooks CL III (2004). J Chem Phys 120

  144. Grycuk T (2003). J Chem Phys 119:4817–4826

    Article  CAS  Google Scholar 

  145. Lee MS, Feig M, Salsbury FR Jr, Brooks CL III (2003). J Comput Chem 24:1348–1356

    PubMed  CAS  Google Scholar 

  146. Kirkwood JG (1934). J Chem Phys 2:351–361

    Article  CAS  Google Scholar 

  147. Lee B, Richards FM (1971). J Mol Biol 55:379

    PubMed  CAS  Google Scholar 

  148. Honig B, Nicholls A (1995). Science 268:1144–1149

    PubMed  CAS  Google Scholar 

  149. Connolly ML (1983). J Appl Crystallogr 16:548–558

    Article  CAS  Google Scholar 

  150. Im W, Lee MS, Brooks CL III (2003). J Comput Chem 24:1691–1702

    PubMed  CAS  Google Scholar 

  151. Nina M, Beglov D, Roux B (1997). J Phys Chem 101:5239–5248

    CAS  Google Scholar 

  152. Banavali NK, Roux B (2002). J Phys Chem B 106:11026–11035

    Article  CAS  Google Scholar 

  153. Zhang W, Hou T, Qiao X, Xu X (2003). J Phys Chem B 107:9071–9078

    Article  CAS  Google Scholar 

  154. Zhu J, Shi Y, Liu H (2002). J Phys Chem B 106:4844–4853

    Article  CAS  Google Scholar 

  155. Dominy BN, Brooks CL III (1999). J Phys Chem B 103:3765–3773

    Article  CAS  Google Scholar 

  156. Calimet N, Schaefer M, Simonson T (2001). Proteins 45:144–158

    PubMed  CAS  Google Scholar 

  157. Tsui V, Case DA (2000). J Am Chem Soc 122:2489–2498

    Article  CAS  Google Scholar 

  158. Lu BZ, Chen WZ, Wang CX, Xu X-j (2002). Proteins 48:497–504

    PubMed  CAS  Google Scholar 

  159. Sharp K (1991). J Comput Chem 12:454–468

    Article  CAS  Google Scholar 

  160. Fogolari F, Brigo A, Molinari H (2003). Biophys J 85:159–166

    PubMed  CAS  Google Scholar 

  161. Prabhu NV, Zhu PJ, Sharp KA (2004). J Comput Chem 25:2049–2064

    PubMed  CAS  Google Scholar 

  162. Feig M, Pettitt BM (1998). Biophys J 75:134–149

    PubMed  CAS  Google Scholar 

  163. Feig M, Pettitt BM (1997). J Phys Chem B 101:7361–7363

    Article  CAS  Google Scholar 

  164. Bursulaya BD, Brooks CL III (2000). J Phys Chem B 104:12378–12383

    Article  CAS  Google Scholar 

  165. Feig M, Pettitt BM (1999). J Mol Biol 286:1075–1095

    PubMed  CAS  Google Scholar 

  166. Berman HM (1994). Curr Opin Struct Biol 4:345–350

    Article  CAS  Google Scholar 

  167. Makarov V, Pettitt BM, Feig M (2002). Acc Chem Res 35:376–384

    PubMed  CAS  Google Scholar 

  168. Pal SK, Zewail AH (2004). Chem Rev 104:2099–2123

    PubMed  CAS  Google Scholar 

  169. Lee MS, Salsbury FR, Olson MA (2004). J Comput Chem 25:1967–1978

    PubMed  CAS  Google Scholar 

  170. Lin J-H, Baker NA, McCammon JA (2002). Biophys J 83:1374–1379

    Article  PubMed  CAS  Google Scholar 

  171. Zhu J, Alexov E, Honig B (2005). J Phys Chem B 109:3008–3022

    Article  CAS  Google Scholar 

  172. Adelman SA, Brooks CL (1982). J Phys Chem 86:1511–1524

    Article  CAS  Google Scholar 

  173. Zagrovic B, Pande V (2003). J Comput Chem 24:1432–1436

    PubMed  CAS  Google Scholar 

  174. Shen M-y, Freed KF (2002). Biophys J 82:1791–1808

    PubMed  CAS  Google Scholar 

  175. Im W, Feig M, Brooks CL III (2003). Biophys J 85:2900–2918

    PubMed  CAS  Google Scholar 

  176. Im W, Brooks CL (2004). J Mol Biol 337:513–519

    PubMed  CAS  Google Scholar 

  177. Spassov VZ, Yan L, Szalma S (2002). J Phys Chem B 106:8726–8738

    Article  CAS  Google Scholar 

  178. Chambers CC, Giese DJ, Hawkins GD, Vaes WH J, Cramer CJ, Truhlar DG (1999). In: Truhlar DG, Howe WJ, Hopfinger AJ, Blaney JM, Dammkoehler RA (eds). Rational drug design. Springer, Berlin Heidelberg New York, pp 51–72

  179. Stern HA, Feller SE (2003). J Chem Phys 118:3401–3412

    Article  CAS  Google Scholar 

  180. Tanizaki S, Feig M (2005). J Chem Phys 122:124706

    PubMed  Google Scholar 

  181. Marrink SJ, Berendsen HJC (1996). J Phys Chem 100:16729–16738

    Article  CAS  Google Scholar 

  182. Marrink SJ, Berendsen HJC (1994). J Phys Chem 98:4155–4168

    Article  CAS  Google Scholar 

  183. Kandt C, Schlitter J, Gerwert K (2004). Biophys J 86:705–717

    PubMed  CAS  Google Scholar 

  184. Baudry J, Tajkhorshid E, Molnar F, Phillips J, Schulten K (2001). J Phys Chem B 105:905–918

    Article  CAS  Google Scholar 

  185. Srinivasan J, Trevathan MW, Beroza P, Case DA (1999). Theor Chim Acta 101:426–434

    CAS  Google Scholar 

  186. Cheng XL, Hornak V, Simmerling C (2004). J Phys Chem B 108:426–437

    Article  CAS  Google Scholar 

  187. Im W, Beglov D, Roux B (1998). Comput Phys Commun 111:59–75

    Article  CAS  Google Scholar 

  188. Roux B (1997). Biophys J 73:2980–2989

    PubMed  CAS  Google Scholar 

  189. Dickerson RE (1998). Nucl Acids Res 26:1906–1926

    PubMed  CAS  Google Scholar 

  190. MacKerell AD Jr, Banavali NK (2000). J Comput Chem 21:105–120

    Article  CAS  Google Scholar 

  191. MacKerell AD Jr, Bashford D, Bellott M, Dunbrack JD, Evanseck MJ, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau F TK, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Reiher WE, Roux B, Schlenkrich M, Smith JC, Stote R, Straub J, Watanabe M, Wiorkiewicz-Kuczera J, Yin D, Karplus M (1998). J Phys Chem B 102:3586–3616

    Article  CAS  Google Scholar 

  192. Foloppe N, MacKerell AD Jr (2000). J Comput Chem 21: 86–104

    Article  CAS  Google Scholar 

  193. Obmolova G, Ban C, Hsieh P, Yang W (2000). Nature 407:703–710

    PubMed  CAS  Google Scholar 

  194. Lamers MH, Perrakis A, Enzlin JH, Winterwerp H HK, de Wind N, Sixma TK (2000). Nature 407:711–717

    PubMed  CAS  Google Scholar 

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Authors and Affiliations

  1. Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824-1319, USA

    Michael Feig, Jana Chocholoušová & Seiichiro Tanizaki

  2. Department of Chemistry, Michigan State University, East Lansing, MI, 48824-1319, USA

    Michael Feig

  3. Department of Computer Science and Engineering, Michigan State University, East Lansing, MI, 48824-1319, USA

    Michael Feig

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  1. Michael Feig
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  3. Seiichiro Tanizaki
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Correspondence to Michael Feig.

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Feig, M., Chocholoušová, J. & Tanizaki, S. Extending the horizon: towards the efficient modeling of large biomolecular complexes in atomic detail. Theor Chem Acc 116, 194–205 (2006). https://doi.org/10.1007/s00214-005-0062-4

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  • DOI: https://doi.org/10.1007/s00214-005-0062-4

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