A new class of models for computing receptor-ligand binding affinities

Chemistry and Biology

Volumn 4, Issue 2, 1997, Pages 87-92

  Gilson, Michael K ^a   Given, James A ^a   Head, Martha S ^a  

^a NATIONAL INSTITUTE OF STANDARDS AND TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0031080551     PISSN: 10745521     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1074-5521(97)90251-9     Document Type: Article

References (76)

1. Hoffman, R. The Same and Not the Same. Columbia University Press, New York, NY, USA.
2. Ajay & Murcko, M.A. (1995). Computational methods to predict binding free energy in ligand-receptor complexes. J. Med Chem. 38, 4953-4967.
3. Wong, C. & McCammon, J.A. (1986). Dynamics and design of enzymes and inhibitors. J. Am. Chem. Soc. 108, 3830-3832.
4. Bash, P.A., Singh, U.C., Langridge, R. & Kollman, P.A. (1987). Free energy calculations by computer simulation. Science 236, 564-568.
5. Beveridge, D.L. & DiCapua, F.M. (1989). Free energy via molecular simulation: application to chemical and biomolecular systems, Annu. Rev. Biophys. Biophys. Chem. 18, 431-492.
6. Lybrand, T. (1990). Computer simulation of biomolecular systems using molecular dynamics and free energy perturbation methods. Rev. Comput. Chem. 1, 295-320.
7. Strastsma, T.P. & McCammon, J.A. (1992). Computational alchemy. Annu. Rev. Phys. Chem. 43, 407-435.
8. Kollman, P. (1993). Free energy calculations - applications to chemical and biochemical phenomena, Chem. Rev. 93, 2395-2417.
9. Warshel, A., Tao, H., Fothergill, M. & Chu, Z.-T. (1994). Effective methods for estimation of binding energies in computer-aided drug design, Isr. J. Chem. 34, 253-256.
10. Marrone, T.J., Briggs, J.M. & McCammon, J.A. (1997). Structure-based drug design: computational advances. Annu. Rev. Pharm. Tox., in press.
11. Mitchell, M.J. & McCammon, J.A. (1991). Free energy difference calculations by thermodynamic integration: difficulties in obtaining a precise value. J. Comput. Chem. 12, 271-275.
12. Balbes, L.M., Mascarella, S.W. & Boyd, D.B. (1994). A perspective of modern methods in computer-aided drug design. Rev, Comput, Chem. 5, 337-379.
13. Chothia, C. & Janin, J. (1975). Principles of protein-protein recognition. Nature 256, 705-708.
14. Andrews, P.R., Craik, D.J. & Martin, J.L (1984). Functional group contributions to drug-receptor interactions. J. Med. Chem. 27, 1648-1657.
15. Erickson, H.P. (1989). Cooperativity in protein-protein association. The structure and stability of the actin filament J. Mol. Biol. 206, 465-474.
16. Novotny, J., Bruccoleri, R.E. & Saul, F.A. (1989). On the attribution of binding energy in antigen-antibody complexes MCPC 603, D1.3 and HyHEL-5. Biochemistry 28, 4735-4749.
17. Searle, M.S., Williams, D.H. & Gerhard, U. (1992). Partitioning of free energy contributions in the estimation of binding constants: residual motions and consequences for amide-amide hydrogen bond strengths. J. Am. Chem. Soc. 114, 10697-10704.
18. Horton, N. & Lewis, M. (1992). Calculation of the free energy of association for protein complexes. Prof. Sci. 1, 169-181.
19. Murphy, K.P., Xie, D., Garcia, K.C., Amzel, L.M., & Freire, E. (1993). Structural energetics of peptide recognition: angiotensin II/antibody binding. Proteins 15, 113-120.
20. Bohm, H.-J. (1994). The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure. J. Comput. Aided Mol. Des. 8, 243-256.
21. Weng, Z., Vajda, S. & DeLisi, C. (1996). Prediction of protein complexes using empirical free energy function. Prof. Sci. 5, 614-626.
22. Gilson, M.K., Given, J.A., Bush, B.L. & McCammon, J.A. (1997). The statistical-thermodynamic basis for computation of binding affinities: a critical review. Biophys. J., in press.
23. Wyman, J. (1965). The binding potential, a neglected linkage concept. J. Mol. Biol. 11, 631-644.
24. Scheilman, J.A. (1975). Macromolecular binding. Biopolymers 14, 999-1018.
25. Appelt, K., et al., & White, J. (1991). Design of enzyme inhibitors using iterative protein crystallographic analysis. J. Med. Chem. 34, 1925-1934.
26. Gilson, M.K. (1993). Multiple-site titration and molecuiar modelling: two rapid methods for computing energies and forces for ionizable groups in proteins. Proteins 15, 266-282.
27. Head, M.S., Given, J.A. & Gilson, M.K. (1997). 'Mining Minima'; direct computation of conformational free energy. J. Phys. Chem., in press.
28. Weiner, S.J., et al. & Weiner, P. (1984), A new force field for molecular mechanical simulation of nucleic acids and proteins. J. Am. Chem. Soc. 106, 765-784.
29. Ferro, D., McQueen, J. & Hermans, J. (1980). Energy minimizations of rubredoxin. J. Mol. Biol. 136, 1-18.
30. Hermans, J., Berendsen, H., van Gunsteren, W. & Postma, J. (1984). A consistent empirical potential for water-protein interactions. Biopolymers 23, 1513-1518.
31. Brooks, B.R., Bruccoleri, R.E., Olafson, B.D., States, D.J., Swaminathan, S. & Karplus, M. (1983). CHARMM: a program for macromolecular energy minimization and dynamics calculations. J. Comput. Chem. 4, 187-217.
32. Maple, J., et al., & Hagler, A. (1994). Derivation of Class II force fields. 1. Methodology and quantum force field for the alkyl functional group and alkane molecules. J. Comput. Chem. 15, 1 162-182.
33. Hwang, M., Stockfisch, T. & Hagler, A. (1994). Derivation of Class II force fields. 2. Derivation and characterization of a Class II forcefield, CFF93, for the alkyl functional group and alkane molecules. J. Am, Chem. Soc. 116, 2515-2525.
34. Maple, J., Hwang, M., Stockfisch, T. & Hagler, A. (1994). Derivation of Class II force fields. 3. Characterization of a quantum force field, for alkanes. Isr. J. Chem. 34, 195-231.
35. van Gunsteren, W.F. & Berendsen, H.J.C. (1987). In Groningen Molecular Simulation (GROMOS) Library Manual. Biomos, Nijenborgh 16, 9747 AG Groningen, The Netherlands.
36. Lii, J. & Allinger, N. (1991). The MM3 force field for amides, polypeptides and proteins. J. Comput. Chem. 12, 186-199.
37. Allinger, N., Kuohsiang, C. & Lii, J. (1996). An improved force field (MM4) for saturated hydrocarbons. J. Comput. Chem. 17, 642-668.
38. Allinger, N.L., Xuefeng, Z. & Bergsma, J. (1994). Molecular mechanics parameters. Theochem. J. Mol. Struct. 118, 69-83.
39. Halgren, T. (1996). Merck Molecular Force Field. I. Basis, form, scope parameterization, and performance of MMFF94. J. Comput. Chem. 17, 490-519.
40. Halgren, T, (1996). Merck Molecular Force Field. II. MMFF94 van der Waals and electrostatic parameters for intermolecular interactions. J. Comput. Chem. 17, 520-552.
41. Halgren, T. (1996). Merck Molecular Force Field, III. Molecular geometries and vibrational frequencies for MMFF94. J. Comput. Chem. 17, 553-586.
42. Halgren, T. (1996). Merck Molecular Force Field. IV. Conformational energies and geometries for MMFF94. J. Comput, Chem. 17, 587-615.
43. Halgren, T. (1996). Merck Molecular Force Field. V. Extension of MMFF94 using experimental data, additional computational data and empirical rules. J. Comput. Chem. 17, 616-641.
44. Kang, Y.K., Gibson, K.D., Nemethy, G. & Scheraga, H.A. (1988). Free energies of hydration oi solute molecules. 4. Revised treatment of the hydration shell model. J. Phys. Chem. 92, 4739-4742.
45. Eisenberg, D, & McLachlan, A.D. (1986). Solvation energy in protein folding and binding. Nature 319, 199-203.
46. Stouten, P.F.W., Frommel, C., Nakamura, H. & Sander, C. (1993). An effective solvation term based on atomic occupancies for use in protein simulations. Mol. Simulat. 10, 97-120.
47. Gilson, M.K. & Honig, B. (1988). Calculation of the total elecirostatic energy of a macromolecular system: solvation energies, binding energies and conformational analysis. Proteins 4, 7-18.
48. Honig, B., Sharp, K. & A.-S Yang. (1993). Macroscopic models of aqueous solutions: biological and chemical applications, J. Phys. Chem. 97, 1101-1109.
49. Still, W.C., Tempczyk, A., Hawley, R.C. & Hendrickson, T. (1990). Semianalytical treatment of solvation for molecular mechanics and dynamics. J. Am. Chem. Soc. 112, 6127-6129.
50. Davis, M.E. (1994). The inducible multipole solvation model: a new model for solvation effects on solute electrostatics. J. Chem. Phys. 100, 5149-5158.
51. Cramer, C. & Truhlar, D. (1995). Continuum solvation models: classical and quantum-mechanical implementations. Rev. Comput. Chem. 6, 1-72.
52. Beglov, D. & Roux, B. (1994), Finite representation of an infinite bulk system: solvent boundary potential for computer simulations. J. Chem. Phys. 100, 9050-9063.
53. Gilson, M.K. (1997). Modeling protonation equilibria in biomolecules. In Computer Simulations of Biomolecular Systems, Escom, in press.
54. Warshel, A., Sussman, F. & King, G. (1986). Free energy of charges in solvated proteins: microscopic calculations using a reversible charging process. Biochemistry 25, 8368-8372.
55. a of Glu 7 and 35 in hen egg white lysozyme and Glu 106 in human carbonic anhydrase II. J. Am. Chem. Soc. 113, 3572-3575.
56. Levy, R.M., Belhadj, M. & Kitchen, D.B. (1991). Gaussian fluctuation formula for electrostatic free-energy changes in solution. J. Chem. Phys. 95, 3627-3633.
57. A.D. MacKerell, Jr, Sommer, M.S. & Karplus, M. (1995). pH-dependence of binding reactions from free energy simulations and macroscopic continuum electrostatic calculations: application to 2′GMP/3′GMP binding to ribonucleaae T1 and implications for catalysis. J. Mol. Biol. 247, 774-807.
58. Matthew, J.B., Gurd, F.R.N., Garcia-Moreno, B,E., Flanagan, M.A., March, K.L & Shire, S.J. (1985). pH-Dependent processes in proteins. Biochemistry 18, 91-197.
59. as of ionizable groups in proteins: atomic detail from a continuum electrostatic model. Biochemistry 29, 327-335,
60. as in proteins. Proteins 15, 252-265.
61. Oberoi, H. & Allewell, N.M. (1993). Multigrid solution of the non-linear Poisson-Boltzmann equation and calculation of titration curves. Biophys. J. 65, 48-55.
62. Antosiewicz, J., McCammon, J.A. & Gilson, M.K. (1994). Prediction of pH-dependent properties of proteins, J. Mol. Biol. 238, 415-436.
63. as of ionizable groups in proteins. J. Phys. Chem. 100, 17373-17387.
64. a calculations. Biophys. J. 71, 138-147.
65. Mehler, E.L. (1996). Self-consistent, free energy based approximation to calculate pH dependent electrostatic effects in proteins. J. Phys. Chem. 100, 16006-16018.
66. Lam, P.Y.S., et al., & Erickson-Viitanen, S, (1994). Rational design of potent, bioavallable, nonpeptide cyclic ureas as HIV protease inhibitors. Science 263, 380-384.
67. Morton, A., Baase, W.A. & Matthews, B.W. (1995), Energetic origins of specificity of ligand binding in an interior nonpolar cavity of T4 lysozyme. Biochemistry 34, 8564-8575.
68. Wang, J. & Purisima, E.O. (1996). Analysis of thermodynamic determinants in helix propensities of nonpolar amino acids through a novel free energy calculation. J. Am. Chem. Soc. 118, 995-1001.
69. Lipkowitz, K.B, & Zegarra, R. (1989), Theoretical studies in molecular recognition: Rebek's cleft, J. Comput. Chem. 10, 595-602.
70. Lipkowitz, K.B., Demeter, D.A., Zegarra, R., Larter, R. & Darden, T. (1988). A protocol for determining enantioselective binding of chiral analytes on chiral Chromatographic surfaces. J. Am. Chem, Soc. 110, 3446-3452.
71. Rosenbluth, M.N. & Rosenbluth, A.W. (1955). Monte Carlo calculation of the average extension of molecular chains. J. Chem. Phys. 23, 356-359.
72. Frenkel, D., Mooij, G. & Smit, B. (1992). Novel scheme to study structural and thermal properties of continuously deformable molecules. J. Phys.-Condens. Matter 4, 3053-3076.
73. Dodd, L., Boone, T. & Theodorou, D. (1993). A concerted rotation algorithm for atomistic Monte Carlo simulation of polymer melts and glasses. Mol. Phys, 78, 961-996.
74. Maginn, E.J., Bell, A.T. & Theodorou, D.N. (1995). Sorption thermodynamics, siting, and conformation of long n-alkanes in silicalite as predicted by configurational-blas Monte Carlo integration, J. Phys. Chem. 99, 2057-2079.
75. Deem, M.W. & Bader, J.S. (1996). A configurational bias Monte Carlo method for linear and cyclic peptides. Mol. Phys. 87, 1245-1260.
76. Wang, J., Szewczuk, Z., Shi-Yi Yue., Tsuda, Y., Konishi, Y. & Purisima, E.O. (1995). Calculation of relative binding free energies and configurational entropies: a structural and thermodynamic analysis of the nature of non-polar binding of thrombin inhibitors based on hirudin. J. Mol. Biol. 253, 473-492.