The statistical-thermodynamic basis for computation of binding affinities: A critical review

被引:973
作者
Gilson, MK
Given, JA
Bush, BL
McCammon, JA
机构
[1] MERCK RES LABS,DEPT MOL DESIGN & DIVERS,RAHWAY,NJ 07065
[2] UNIV CALIF SAN DIEGO,DEPT CHEM & BIOCHEM,LA JOLLA,CA 92093
[3] UNIV CALIF SAN DIEGO,DEPT PHARMACOL,LA JOLLA,CA 92093
基金
美国国家科学基金会; 美国国家卫生研究院;
关键词
D O I
10.1016/S0006-3495(97)78756-3
中图分类号
Q6 [生物物理学];
学科分类号
071011 ;
摘要
Although the statistical thermodynamics of noncovalent binding has been considered in a number of theoretical papers, few methods of computing binding affinities are derived explicitly from this underlying theory. This has contributed to uncertainty and controversy in certain areas. This article therefore reviews and extends the connections of some important computational methods with the underlying statistical thermodynamics. A derivation of the standard free energy of binding forms the basis of this review. This derivation should be useful in formulating novel computational methods for predicting binding affinities. It also permits several important points to be established. For example, it is found that the double-annihilation method of computing binding energy does not yield the standard free energy of binding, but can be modified to yield this quantity. The derivation also makes it possible to define clearly the changes in translational, rotational, configurational, and solvent entropy upon binding. It is argued that molecular mass has a negligible effect upon the standard free energy of binding for biomolecular systems, and that the cratic entropy defined by Gurney is not a useful concept. In addition, the use of continuum models of the solvent in binding calculations is reviewed, and a formalism is presented for incorporating a limited number of solvent molecules explicitly.
引用
收藏
页码:1047 / 1069
页数:23
相关论文
共 121 条
  • [1] Computational methods to predict binding free energy in ligand-receptor complexes
    Ajay
    Murcko, MA
    [J]. JOURNAL OF MEDICINAL CHEMISTRY, 1995, 38 (26) : 4953 - 4967
  • [2] RECOMMENDATIONS FOR NOMENCLATURE AND TABLES IN BIOCHEMICAL THERMODYNAMICS
    ALBERTY, RA
    CORNISHBOWDEN, A
    GIBSON, QH
    GOLDBERG, RN
    HAMMES, GG
    JENCKS, W
    TIPTON, KF
    VEECH, R
    WESTERHOFF, HV
    WEBB, EC
    [J]. PURE AND APPLIED CHEMISTRY, 1994, 66 (08) : 1641 - 1666
  • [3] CLUSTER EXPANSIONS FOR HYDROGEN-BONDED FLUIDS .1. MOLECULAR ASSOCIATION IN DILUTE GASES
    ANDERSEN, HC
    [J]. JOURNAL OF CHEMICAL PHYSICS, 1973, 59 (09) : 4714 - 4725
  • [4] FUNCTIONAL-GROUP CONTRIBUTIONS TO DRUG RECEPTOR INTERACTIONS
    ANDREWS, PR
    CRAIK, DJ
    MARTIN, JL
    [J]. JOURNAL OF MEDICINAL CHEMISTRY, 1984, 27 (12) : 1648 - 1657
  • [5] DESIGN OF ENZYME-INHIBITORS USING ITERATIVE PROTEIN CRYSTALLOGRAPHIC ANALYSIS
    APPELT, K
    BACQUET, RJ
    BARTLETT, CA
    BOOTH, CLJ
    FREER, ST
    FUHRY, MAM
    GEHRING, MR
    HERRMANN, SM
    HOWLAND, EF
    JANSON, CA
    JONES, TR
    KAN, CC
    KATHARDEKAR, V
    LEWIS, KK
    MARZONI, GP
    MATTHEWS, DA
    MOHR, C
    MOOMAW, EW
    MORSE, CA
    OATLEY, SJ
    OGDEN, RC
    REDDY, MR
    REICH, SH
    SCHOETTLIN, WS
    SMITH, WW
    VARNEY, MD
    VILLAFRANCA, JE
    WARD, RW
    WEBBER, S
    WEBBER, SE
    WELSH, KM
    WHITE, J
    [J]. JOURNAL OF MEDICINAL CHEMISTRY, 1991, 34 (07) : 1925 - 1934
  • [6] ATKINS PW, 1994, PHYSICAL CHEM
  • [7] BALBES LM, 1994, REV COMP CH, V5, P337, DOI 10.1002/9780470125823.ch7
  • [8] FREE-ENERGY CALCULATIONS BY COMPUTER-SIMULATION
    BASH, PA
    SINGH, UC
    LANGRIDGE, R
    KOLLMAN, PA
    [J]. SCIENCE, 1987, 236 (4801) : 564 - 568
  • [9] BASHFORD D, 1990, BIOCHEMISTRY-US, V9, P327
  • [10] FINITE REPRESENTATION OF AN INFINITE BULK SYSTEM - SOLVENT BOUNDARY POTENTIAL FOR COMPUTER-SIMULATIONS
    BEGLOV, D
    ROUX, B
    [J]. JOURNAL OF CHEMICAL PHYSICS, 1994, 100 (12) : 9050 - 9063