中文
Earlier issues
Announcement
More
Progress in Chemistry 2004, Vol. 16 Issue (02): 153- Previous Articles   Next Articles

Special Issue: 计算化学

• Review •

Calculations of Free Energies Based on the Combination of Molecular Dynamics Simulations and Continuum Solvation Model

Hou Tingjun;Xu Xiaojie**   

  1. (College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China)
  • Received: Revised: Online: Published:
  • Contact: Xu Xiaojie
PDF ( 4138 ) Cited
Export

EndNote

Ris

BibTeX

In recent years, the methods of calculating free energies based on the combination of molecular dynamics simulations and continuum solvation models have drawn more and more attention, in which MM/PBSA is the most repre-sentational one. In MM/PBSA, the sum of molecular mechanical energies of the molecules is calculated from molecular mechanics (MM); the polar solvation energy in continuum solvent is usually computed using a finite-difference Poisson-Boltzmann (PB) model; and the nonpolar solvation energy is often obtained from the solvent-accessible surface area (SA). In this paper, the progress and application of MM/PBSA, as well as some research works in our group, are intro-duced.
Key words: free energy, MM/PBSA, continuum solvation model

CLC Number: 

[ 1 ] van Gunsteren W F. Protein Eng. , 1988 , 2 : 5 —13
[ 2 ] Jorgensen W L. Acc. Chem. Res. , 1989 , 22 : 184 —189
[ 3 ] Kollman P. Chem. Rev. , 1993 , 93 : 2395 —2417
[ 4 ] Beveridge D L , Di Capua F M. Annu. Rev. Biophys. Biophys. ,1989 , 18 : 431 —492
[ 5 ] Pearlman D A , Kollman P A. J . Chem. Phys. , 1989 , 91 :7831 —7839
[ 6 ] Pearlman D A , Kollman P A. J . Chem. Phys. , 1991 , 94 :4532 —4545
[ 7 ] Pearlman D. J . Comp. Chem. , 1994 , 15 : 105 —123
[ 8 ] Radmer R J , Kollman P A. J . Comp. Chem. , 1997 , 18 : 902 —919
[ 9 ] Cox J P L , Nicholls I A , Williams D H. J . Chem. Soc. , Chem.Comm. , 1991 , 18 : 1295 —1299
[10] Searle M S , Williams D H , Gerhard U. J . Am. Chem. Soc. ,1992 , 114 : 10697 —10704
[11] Williams D H , Searle M S , Mackay J P , Gerhard U , Maplestone R A. Proc. Natl . Acad. Sci . USA , 1993 , 90 : 1172 —1176
[12] Krystek S , Stouch T, Novotny J . J . Mol . Biol . , 1993 , 234 :661 —679
[13] Klebe G, Bohm H J . J . Recept . Signal . Tr. R. , 1997 , 17 :459 —473
[14] Bohm H J . J . Comput . -Aided. Mol . Des. , 1998 , 12 : 309 —323
[15] Head R D , Smythe M L , Oprea T I , Waller C L , Greene S M,Marshall G R. J . Am. Chem. Soc. , 1996 , 118 : 3959 —3969
[16] Edlridge M D , Murray C W, Auto T R , Paolini GV , Mee R P.J . Comput .-Aided Mol . Des. , 1997 , 11 : 425 —445
[17] Shoichet K, Kuntz I D. J . Mol . Biol . , 1991 , 221 : 327 —346
[18] Luty B A , Wasserman Z R , Stouten P F W, Hodge C N , Zacharias M, McCammon J A. J . Comp. Chem. , 1995 , 16 : 454 —464
[19] Hou T J , Wang J M, Chen L R , Xu X J . Protein Eng. , 1999 ,12 : 639 —647
[20] Srinivasan J , Cheatham T E , Cieplak P , Kollman P A , Case D A. J . Am. Chem. Soc. , 1998 , 120 : 9401 —9409
[21] Vorobjev Y N , Almagro J C , Hermans J . Proteins : Struct . ,Funct . Genet . , 1998 , 32 : 399 —413
[22] Jayaram B , Sprous D , Young M A , Beveridge D L. J . Am.Chem. Soc. , 1998 , 120 : 10629 —10633
[23] Chong L T, Duan Y, Wang L , Massova I , Kollman P A. Proc.Natl . Acad. Sci . USA , 1999 , 96 : 14330 —14335
[24] Reyes C M, Kollman P A. J . Mol . Biol . , 2000 , 295 : 1 —6
[25] Massova I , Kollman P A. Perspect . Drug Discov. , 2000 , 18 :113 —135
[26] Kuhn B , Kollman P A. J . Med. Chem. , 2000 , 43 : 3786 —3791
[27] Donini O A T, Kollman P A. J . Med. Chem. , 2000 , 43 :4180 —4188
[28] Wang W, Kollman P A. J . Mol . Biol . , 2000 , 303 : 567 —582
[29] Kollman P A , Massova I , Reyes C , Kuhn B , Huo S H , ChongL ,Lee M, Lee T, Duan Y, Wang W, Donini O , Cieplak P , Srinivasan J , Case D A , Cheatham T E. Accounts Chem. Res. , 2000 ,33 : 889 —897
[30] Wang J M, Morin P , Wang W, Kollman P A. J . Am. Chem.Soc. , 2001 , 123 : 5221 —5230
[31] Hou T J , Guo S L , Xu X J . J . Phys. Chem. B , 2002 , 106 :5527 —5535
[32] 侯廷军(Hou T J ) , 朱丽荔(Zhu L L) , 陈丽蓉(Chen L R) , 徐筱杰(Xu X J ) . 化学学报(Acta Chim. Sinica) , 2002 , 60 :1023 —1028
[33] Hou T J , Zhu L L , Chen L R , Xu X J . J . Chem. Inf . Comput .Sci . , 2003 , 43 : 273 —287
[34] Hou T J , Qiao X B , Xu X J , Zhang L , Yu H W, Zhang H Y,Zhang L H. J . Mol . Modl . (in press)
[35] Hou T J , Qiao X B , Xu X J . J . Phys. Chem. B , 2002 , 106 :11295 —11304
[36] 侯廷军(Hou T J ) , 徐筱杰(Xu X J ) . 物理化学学报(Acta Phys. Chim. Sin. ) , 2002 , 18 : 1052 —1055
[37] Honig B , Nicholls A. Science , 1995 , 268 : 1144 —1149
[38] Hecht J L , Honig B , Shin Y K, Hubbell WL. J . Phys. Chem. ,1995 , 99 : 7782 —7786
[39] Sanner M F , Olson A J , Spehner J . Biopolymers , 1996 , 38 :305 —320
[40] Wilson E B , Decius J C , Cross P C. Molecular Vibrations. New York : McGraw-Hill , 1955
[41] Stamos J , Sliwkowski M X, Eigenbrot C. J . Biol . Chem. , 2002 ,277 : 46265 —46272
[42] Constanciel R , Contreras R. Theor. Chim. Acta , 1984 , 65 : 1 —11
[43] Still W C , Hawley R C , Hendrickson T. J . Am. Chem. Soc. ,1990 , 112 : 6127 —6129
[44] Schaefer M. Karplus M. J . Phys. Chem. , 1996 , 100 : 1578 —1599
[1] Haochuan Chen, Haohao Fu, Xueguang Shao, Wensheng Cai. Importance Sampling Methods and Free Energy Calculations [J]. Progress in Chemistry, 2018, 30(7): 921-931.
[2] Lingang Hou, Lili Ma, Yichen Zhou, Yu Zhao, Yi Zhang, Jinmei He*. Application of Low Surface Energy Compounds to the Superwetting Materials [J]. Progress in Chemistry, 2018, 30(12): 1887-1898.
[3] Fang Sheng. Viscosity Model for Mixtures Based on Eyring’s Absolute Reaction Theory [J]. Progress in Chemistry, 2010, 22(0203): 309-314.
[4] Qinghua Li Jingwei Wang Hao Yuan Lili Xie Lijun Wang Alexandra Navrotsky . Thermochemistry of Microporous and Mesoporous Materials [J]. Progress in Chemistry, 2006, 18(05): 680-686.
[5] Gu Guotuan1,2,Zhang Zhijun2** ,Dang Hongxin1,2. Fabrications and Applications of Low Surface Free Energy Surfaces [J]. Progress in Chemistry, 2002, 14(03): 158-.