Free energy calculations: Use and limitations in predicting ligand binding affinities

Reviews in Computational Chemistry

Volumn 16, Issue , 2000, Pages 217-304

  Rami Reddy, M ^a   Erion, Mark D ^a   Agarwal, Atul ^a  

^a Metabasis Therapeutics Inc   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 19644371654     PISSN: 10693599     EISSN: None     Source Type: Book Series    
DOI: None     Document Type: Article

References (310)

1. M. R. Reddy and A. L. Parrill, in Rational Drug Design: Novel Methodology and Practical Applications, ACS Symposium Series 719, A. L. Parrill and M. R. Reddy, Eds., Oxford University Press, Washington, DC, 1999, pp. 1-11. Overview of Rational Drug Design.
2. D. B. Boyd, in Rational Drug Design: Novel Methodology and Practical Applications, ACS Symposium Series 719, A. L. Parrill and M. R. Reddy, Eds., Oxford University Press, Washington, DC, 1999, pp. 346-356. Is Rational Design Good for Anything?
3. R. J. Zwanzig, J. Chem. Phys., 22, 1420 (1954). High-Temperature Equation of State by a Perturbation Method. I. Nonpolar Gases.
4. D. L. Beveridge and F. M. DiCapua, Annu. Rev. Biophys. Biophys. Chem., 18, 431 (1989). Free Energy Via Molecular Simulation Applications to Chemical and Biomolecular Systems.
5. T. P. Lybrand, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., VCH Publishers, New York, 1990, Vol. 1, pp. 295-315. Computer Simulation of Biomolecular Systems Using Molecular Dynamics and Free Energy Perturbation Methods.
6. D. A. Pearlman and B. G. Rao, in Encyclopedia of Computational Chemistry, P. v. R. Schleyer, Ed., Wiley, New York, 1999, Vol. 2, pp. 1036-1061. Free Energy Calculations: Methods and Applications.
7. T. P. Straatsma, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., VCH Publishers, New York, 1996, Vol. 9, pp. 81-127. Free Energy by Molecular Simulation.
8. H. Meirovitch, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., Wiley-VCH, New York, 1998, Vol. 12, pp. 1-74. Calculation of the Free Energy and the Entropy of Macromolecular Systems by Computer Simulation.
9. M. R. Reddy, M. D. Varney, V. Kalish, V. N. Viswanadhan, and K. Appelt, J. Med. Chem., 37, 1145 (1994). Calculation of Relative Differences in the Binding Free Energies of HIV1 Protease Inhibitors: A Thermodynamic Cycle Perturbation Approach.
10. D. A. McQuarrie, Statistical Mechanics, Harper & Row, New York, 1976.
11. G. Herzberg, in Molecular Spectra and Molecular Structure, G. Herzberg, Ed., Van Nostrand, New York, 1945, Vol. 2, pp. 501-530. Infrared and Raman Spectra of Polyatomic Molecules.
12. U. C. Singh, P. Weiner, J. Caldwell, and P. A. Kollman, University of California, San Francisco, CA, 1986. AMBER 3.0.
13. D. A. Pearlman, D. A. Case, J. W. Caldwell, G. L. Seibel, U. C. Singh, P. A. Weiner, and P. A. Kollman, University of California, San Francisco, CA, 1991. AMBER 4.0.
14. L. Nilsson and M. Karplus, J. Comput. Chem., 7, 591 (1986). Empirical Energy Functions for Energy Minimization and Dynamics of Nucleic Acids.
15. U. Dinur and A. T. Hagler, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., VCH Publishers, New York, 1991, Vol. 2, pp. 99-164. New Approaches to Empirical Force Fields.
16. T. A. Halgren, J. Comput. Chem., 17, 490 (1996). Merck Molecular Force Field. I. Basis, Form, Scope, Parameterization, and Performance of MMFF94.
17. Theory Manual, SYBYL 6.5, Tripos Inc., St. Louis, MO, 1995.
18. J. E. H. Koehler, W. Saenger, and W. F. van Gunsteren, Eur. Biophys. J., 15, 197 (1987). A Molecular Dynamics Simulation of Crystalline α-Cyclodextrin Hexahydrate.
19. W. L. Jorgensen and J. Tirado-Rives, J. Am. Chem. Soc., 110, 1657 (1988). The OPLS Potential Functions for Proteins: Energy Minimizations for Crystals of Cyclic Peptides and Crambin.
20. Discover User Guide, Part 1, Versions 2.9.5 and 94.0. BIOSYM Technologies (now part of Molecular Simulations, Inc.), San Diego, CA, 1994.
21. J. Hermans, H. J. C. Berendsen, W. F. van Gunsteren, and J. P. M. Postma, Biopolymers, 23, 1513 (1984). A Consistent Empirical Potential for Water-Protein Interactions.
22. N. L. Allinger, J. Am. Chem. Soc., 99, 8127 (1977). Conformational Analysis. 130. MM2, a Hydrocarbon Force Field Utilizing V1 and V2 Torsional Terms.
23. N. L. Allinger, Y. H. Yuh, and J.-H. Lii, J. Am. Chem. Soc., 111, 8551 (1989). Molecular Mechanics: The MM3 Force Field for Hydrocarbons. 1.
24. J. P. Bowen and N. L. Allinger, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., VCH Publishers, New York, 1991, Vol. 2, pp. 81-97. Molecular Mechanics: The Art and Science of Parameterization.
25. L. Onsager, J. Am. Chem. Soc., 58, 1486 (1936). Electric Moments of Molecules in Liquids.
26. J. A. Barker and R. O. Watts, Mol. Phys., 26, 789 (1973). Monte Carlo Studies of the Dielectric Properties of Water-like Models.
27. A. Warshel and S. T. Russell, Q. Rev. Biophys., 17, 283 (1984). Calculations of Electrostatic Interactions in Biological Systems and in Solutions.
28. S. T. Russell and A. Warshel, J. Mol. Biol., 185, 389 (1985). Calculations of Electrostatic Energies in Proteins: The Energetics of Ionized Groups in Bovine Pancreatic Trypsin Inhibitor.
29. P. P. Ewald, Ann. Phys., 64, 253 (1921). Die Berechnung optischer und elektrostatischer Gitterpotentiale.
30. F. J. Vesely, J. Comput. Phys., 24, 361 (1977). N-Particle Dynamics of Polarizable Stockmayer-Type Molecules.
31. W. F. van Gunsteren and H. J. C. Berendsen, in Molecular Dynamics and Protein Structure, J. Hermans, Ed., University of North Carolina Printing Department, West Springs, NC, 1985, pp. 5-14. Molecular Dynamics Simulations: Techniques and Applications to Proteins.
32. W. F. van Gunsteren and H. J. C. Berendsen, Mol. Phys., 34, 1311 (1977). Algorithms for Macromolecular Dynamics and Constraint Dynamics.
33. J. P. Ryckaert, G. Ciccotti, and H. J. C. Berendsen, J. Comput. Phys., 23, 327 (1977). Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes.
34. R. Kutteh and T. P. Straatsma, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., Wiley-VCH, New York, 1998, Vol. 12, pp. 75-136. Molecular Dynamics with General Holonomic Constraints and Application to Internal Coordinate Constraints.
35. W. F. van Gunsteren and M. Karplus, Biochemistry, 21, 2259 (1982). Protein Dynamics in Solution and in a Crystalline Environment: A Molecular Dynamics Study.
36. T. Darden, D. York, and L. Pederson, J. Chem. Phys., 98, 10089 (1993). Particle Mesh Ewald: An N log(N) Method for Ewald Sums in Large Systems.
37. D. J. Adams, Chem. Phys. Lett., 62, 329 (1979). Computer Simulations of Ionic Systems: The Distorting Effects of the Boundary Conditions.
38. K. A. Sharp, in Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications, W. F. van Gunsteren, P. K. Weiner, and A. J. Wilkinson, Eds., ESCOM, Leiden, 1993, Vol. 2, pp. 147-160. Inclusion of Solvent Effects in Molecular Mechanics Force Fields.
39. C. J. Cramer and D. G. Truhlar, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., VCH Publishers, New York, 1995, Vol. 6, pp. 1-72. Continuum Solvation Models: Classical and Quantum Mechanical Implementations.
40. G. C. Lie and E. Clementi, J. Chem. Phys., 62, 2195 (1975). Study of the Structure of Molecular Complexes. XII. Structure of Liquid Water Obtained by Monte Carlo Simulation with the Hartree-Fock Potential Corrected by Inclusion of Dispersion Forces.
41. F. H. Stillinger and A. Rahman, J. Chem. Phys., 60, 1545 (1974). Improved Simulation of Liquid Water by Molecular Dynamics.
42. W. L. Jorgensen, J. Am. Chem. Soc., 103, 335 (1981). Transferable Intermolecular Potential Functions for Water, Alcohols, and Ethers: Application to Liquid Water.
43. W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein, J. Chem. Phys., 79, 926 (1983). Comparison of Simple Potential Functions for Simulating Liquid Water.
44. H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, and J. Hermans, in Intermolecular Forces, B. Pullman, Ed., Reidel, Boston, 1981, pp. 331-342. Interaction Models for Water in Relation to Protein Hydration.
45. H. J. C. Berendsen, J. R. Grigera, and T. P. Straatsma, J. Phys. Chem., 91, 6269 (1987). The Missing Term in Effective Pair Potentials.
46. A. Wallqvist and R. D. Mountain, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., Wiley-VCH, New York, 1999, Vol. 13, pp. 183-247. Molecular Models of Water: Derivation and Description.
47. M. R. Reddy and M. Berkowitz, Chem. Phys. Lett., 155, 173 (1989). The Dielectric Constant of SPC/E Water.
48. W. C. Still, A. Tempczyk, R. C. Hawley, and T. Hendrickson, J. Am. Chem. Soc., 112, 6127 (1990). Semianalytical Treatment of Solvation for Molecular Mechanics and Dynamics.
49. B. L. Tembe and J. A. McCammon, Comput. Chem., 8, 281 (1984). Ligand-Receptor Interactions.
50. W. F. van Gunsteren and P. K. Weiner, Computer Simulation of Biomolecular Systems, ESCOM, Leiden, 1989.
51. M. R. Reddy, V. N. Viswanadhan, and J. N. Weinstein, Proc. Natl. Acad. Sci. USA, 88, 10287 (1991). Relative Differences in the Binding Free Energies of Human Immunodeficiency Virus 1 Protease Inhibitors: A Thermodynamic Cycle-Perturbation Approach.
52. a Calculations and the Hydration of Organic Anions.
53. P. I. Nagy, G. J. Durant, and D. A. Smith, J. Am. Chem. Soc., 115, 2912 (1993). Theoretical Studies on Hydration of Pyrrole, Imidazole and Protonated Imidazole in the Gas Phase and Aqueous Solution.
54. P. A. Bash, U. C. Singh, R. Langridge, and P. A. Kollman, Science, 236, 564 (1987). Free Energy Calculations by Computer Simulation.
55. P. Cieplak, P. Bash, U. C. Singh, and P. A. Kollman, J. Am. Chem. Soc., 109, 6283 (1987). A Theoretical Study of Tautomerization in the Gas Phase and Aqueous Solution: A Combined Use of "State-of-the-Art" Ab Initio Quantum Mechanics and Free Energy Perturbation Methods.
56. 6-Dimethyl-2,6-Diaminobenz[cd]indole in the Gas Phase and in Aqueous Solution: A Combined Quantum Mechanical and Free Energy Perturbation Study.
57. M. R. Reddy, M. D. Erion, A. Agarwal, V. N. Viswanadhan, D. Q. McDonald, and W. C. Still, J. Comput. Chem., 19, 769 (1998). Solvation Free Energies Calculated Using the GBJSA Model: Sensitivity of Results on Charge Sets, Protocols, and Force Fields.
58. M. J. Mitchell and J. A. McCammon, J. Comput. Chem., 12, 271 (1991). Free Energy Difference Calculations by Thermodynamic Integration: Difficulties in Obtaining a Precise Value.
59. D. A. Pearlman and P. A. Kollman, J. Chem. Phys., 94, 4532 (1991). The Overlooked-Stretching Contribution in Free Energy Perturbation Calculations.
60. F. Guarnieri and W. C. Still, J. Comput. Chem., 15, 1302 (1994). A Rapidly Convergent Simulation Method: Mixed Monte Carlo/Stochastic Dynamics.
61. D. A. Pearlman, J. Comput. Chem., 15, 105 (1994). Free Energy Derivatives: A New Method for Probing the Convergence Problem in Free Energy Calculations.
62. C. Chipot, C. Millot, B. Maigret, and P. A. Kollman, J. Phys. Chem., 98, 11362 (1994). Molecular Dynamics Free Energy Perturbation Calculations: Influence of Nonbonded Parameters on the Free Energy of Hydration of Charged and Neutral Species.
63. C. Chipot, P. A. Kollman, and D. A. Pearlman, J. Comput. Chem., 17, 1112 (1996). Alternative Approaches to Potential of Mean Force Calculations: Free Energy Perturbation Versus Thermodynamic Integration: Case Study of Some Representative Nonpolar Interactions.
64. M. R. Reddy and M. D. Erion, J. Comput. Chem., 20, 1018 (1999). Calculation of Relative Solvation Free Energy Differences by Thermodynamic Perturbation Method: Dependence of the Free Energy Results on the Simulation Length.
65. M. R. Reddy, R. J. Bacquet, D. Zichi, D. A. Matthews, K. M. Welsh, T. R. Jones, and S. Freer, J. Am. Chem. Soc., 114, 10117 (1992). Calculation of Solvation and Binding Free Energy Differences for Folate-Based Inhibitors of the Enzyme Thymidylate Synthase.
66. M. M. Francl and L. E. Chirlian, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., Wiley-VCH, New York, 2000, Vol. 14, pp. 1-31. The Pluses and Minuses of Mapping Atomic Charges to Electrostatic Potentials.
67. G. A. Worth, P. M. King, and W. G. Richards, Biochim. Biophys. Acta, 993, 134 (1989). Theoretical Calculation of Tautomer Equilibria in Solution: 4-(5-)-Methylimidazole.
68. G. A. Worth, P. M. King, and W. G. Richards, Biochim. Biophys. Acta, 1036, 158 (1990). Histamine Tautomerism and Its Mode of Action.
69. G. A. Worth and W. G. Richards, J. Am. Chem. Soc., 116, 239 (1994). Calculation of the Tautomer Ratio of Histamine in Aqueous Solution Using Free Energy Perturbation Methods: An In-Depth Study.
70. J. R. Cox, S. Woodcock, I. H. Hillier, and M. A. Vincent, J. Phys. Chem., 94, 5499 (1990). Tautomerism of 1,2,3-Triazole and 1,2,4-Triazole in the Gas Phase and in Aqueous Solution - A Combined Ab Initio Quantum Mechanics and Free Energy Perturbation Study.
71. O. G. Parchment, D. V. S. Green, P. J. Taylor, and I. H. Hillier, J. Am. Chem. Soc., 115, 2352 (1993). The Prediction of Tautomer Equilibria in Hydrated 3-Hydroxypyrazole: A Challenge to Theory.
72. P. I. Nagy, G. J. Durant, W. P. Hoss, and D. A. Smith, J. Am. Chem. Soc., 116, 4898 (1994). Theoretical Analyses of the Tautomeric and Conformational Equilibria of Histamine and (aR,bS)-ab-Dimethylhistamine in the Gas Phase and Aqueous Solution.
73. M. Orozco and F. J. Luque, J. Am. Chem. Soc., 117, 1378 (1995). Theoretical Study of the Tautomerism and Protonation of 7-Aminopyrazolopyrimidine in the Gas Phase and in Aqueous Solution.
74. a of Ethane.
75. P. M. King, C. A. Reynolds, and W. G. Richards, J. Mol. Struct. (THEOCHEM), 208, 205 (1990). The Theoretical Calculation of Basicities: An Homologous Amine Series.
76. J. M. Briggs and J. Antosiewicz, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., Wiley-VCH, New York, 1999, Vol. 13, pp. 249-311. Simulation of pH-Dependent Properties of Proteins Using Mesoscopic Models.
77. R. F. Rekker and R. Mannhold, Calculation of Drug Lipophilicity, VCH Publishers, New York, 1992.
78. P.-A. Carrupt, B. Testa, and P. Gaillard, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., Wiley-VCH, New York, 1997, Vol. 11, pp. 241-315. Computational Approaches to Lipophilicity: Methods and Applications.
79. V. N. Viswanadhan, M. R. Reddy, R. J. Bacquet, and M. D. Erion, J. Comput. Chem., 14, 1019 (1993). Assessment of Methods Used for Predicting Lipophilicity: Application to Nucleosides and Nucleoside Bases.
80. N. Bodor and M.-J. Huang, J. Pharmacol. Sci., 81, 272 (1992). An Extended Version of a Novel Method for the Estimation of Partition Coefficients.
81. A. J. Leo, Daylight Chemical Information Systems, Irvine, CA, 1991. CLOGP. (Also available from Biobyte, Claremont, CA).
82. A. K. Ghose and G. M. Crippen, J. Comput. Chem., 7, 565 (1986). Atomic Physicochemical Parameters for Three-Dimensional Structure-Directed Quantitative Structure-Activity Relationships. I. Partition Coefficients as a Measure of Hydrophobicity.
83. A. K. Ghose, A. Pritchett, and G. M. Crippen, J. Comput. Chem., 9, 80 (1988). Atomic Physicochemical Parameters for Three Dimensional Structure Directed Quantitative Structure-Activity Relationships. III. Modeling Hydrophobic Interactions.
84. M. R. Reddy, M. D. Erion, V. N. Viswanadhan, and A. Agarwal, to be published. GLOGP: A New Algorithm for the Estimation of log P for Organic and Biological Molecules.
85. J. W. Essex, C. A. Reynolds, and W. G. Richards, J. Chem. Soc., Chem. Commun., 1152 (1989). Relative Partition Coefficients from Partition Functions: A Theoretical Approach to Drug Transport.
86. W. L. Jorgensen, J. M. Briggs, and M. L. Contreras, J. Phys. Chem., 94, 1683 (1990). Relative Partition Coefficients for Organic Solutes from Fluid Simulations.
87. E. M. Duffy, D. L. Severance, and W. L. Jorgensen, Isr. J. Chem., 33, 323 (1993). Urea: Potential Functions, log P, and Free Energy of Hydration.
88. J. W. Essex, C. A. Reynolds, and W. G. Richards, J. Am. Chem. Soc., 114, 3634 (1992). Theoretical Determination of Partition Coefficients.
89. S. E. DeBolt and P. A. Kollman, J. Am. Chem. Soc., 117, 5316 (1995). Investigation of Structure, Dynamics, and Solvation in 1-Octanol and Its Water-Saturated Solution: Molecular Dynamics and Free-Energy Perturbation Studies.
90. X. Daura, P. H. Hunenberger, A. E. Mark, E. Querol, F. X. Aviles, and W. F. van Gunsteren, J. Am. Chem. Soc., 118, 6285 (1996). Free Energies of Transfer of Trp Analogs from Chloroform to Water: Comparison of Theory and Experiment and the Importance of Adequate Treatment of Electrostatic and Internal Interactions.
91. A. Miklavc and D. Hadzi, in QSAR, Rational Approaches to the Design of Bioactive Compounds: Proceedings of the Eighth European Symposium on Quantitative Structure-Activity Relationships, C. Silipo and A. Vittoria, Eds., Elsevier Science Publishers, Amsterdam, 1991, pp. 71-00. Delineating the Role of Hydrophobicity in Quantitative Structure-Activity Relationships.
92. K. B. Wiberg, K. M. Morgan, and H. Maitz, J. Am. Chem. Soc., 116, 11067 (1994). Thermochemistry of Carbonyl Reactions. 6. A Study of Hydration Equilibria.
93. M. D. Erion and M. R. Reddy, J. Comput. Chem., 16, 1513 (1995). Calculation of Relative Free Energy Differences for the Covalent Hydration of Organic Compounds: A Combined Quantum Mechanical and Free Energy Perturbation Study.
94. M. D. Erion and M. R. Reddy, J. Am. Chem. Soc., 120, 3295 (1998). Calculation of Relative Hydration Free Energy Differences for Heteroaromatic Compounds: Use in the Design of Adenosine Deaminase and Cytidine Deaminase Inhibitors.
95. M. D. Erion and M. R. Reddy, in Rational Drug Design: Novel Methodology and Practical Applications, ACS Symposium Series 719, A. L. Parrill and M. R. Reddy, Eds., Oxford University Press, Washington, DC, 1999, pp. 107-120. Calculation of Relative Hydration Free Energy Differences for Heteroaromatic Compounds: Use in the Design of AMP Deaminase Inhibitors.
96. W. L. Jorgensen and C. Ravimohan, J. Chem. Phys., 83, 3050 (1985). Monte Carlo Simulation of Differences in Free Energies of Hydration.
97. 3) in the Gas Phase.
98. T. P. Straatsma and J. A. McCammon, J. Chem. Phys., 91, 3631 (1989). Treatment of Rotational Isomers in Free Energy Calculations. II. Molecular Dynamics Simulation Study of 18-Crown-6 in Aqueous Solution as an Example of Systems with Large Numbers of Rotational Isomeric States.
99. C. L. Brooks, Int. J. Quantum. Chem., Quantum. Biol. Symp., 15, 221 (1988). Thermodynamic Calculations in Biological Molecules.
100. - from Statistical Perturbation Theory.
101. B. G. Rao and U. C. Singh, J. Am. Chem. Soc., 111, 3125 (1989). Hydrophobic Hydration: A Free Energy Perturbation Study.
102. K. Ramnarayan, B. G. Rao, and U. C. Singh, J. Chem. Phys., 92, 7057 (1990). The Effect of Polarization Energy on the Free Energy Perturbation Calculations.
103. S. E. DeBolt and P. A. Kollman, J. Am. Chem. Soc., 112, 7515 (1990). Theoretical Examination of Solvatochromism and Solute-Solvent Structuring in Simple Alkyl Carbonyl Compounds. Simulations Using Statistical Mechanical Free Energy Perturbation Methods.
104. M. A. S. Saqi and J. M. Goodfellow, Protein Eng., 3, 419 (1990). Free Energy Changes Associated with Amino Acid Substitution in Proteins.
105. L. F. Kuyper, R. N. Hunter, D. Ashton, K. M. Merz Jr., and P. A. Kollman, J. Phys. Chem., 95, 6661 (1991). Free Energy Calculations on the Relative Solvation Free Energies of Benzene, Anisole, and 1,2,3-Trimethoxybenzene: Theoretical and Experimental Analysis of Aromatic Methoxy Solvation.
106. Y. Sun, D. Spellmeyer, D. A. Pearlman, and P. A. Kollman, J. Am. Chem. Soc., 114, 6798 (1992). Simulation of the Solvation Free Energies for Methane, Ethane, and Propane and Corresponding Amino Acid Dipeptides: A Critical Test of the "Bond-PMF" Correction, a New Set of Hydrocarbon Parameters, and the Gas Phase-Water Hydrophobicity Scale.
107. C. A. Gough, D. A. Pearlman, and P. A. Kollman, J. Chem. Phys., 99, 9103 (1993). Calculations of the Relative Free Energies of Aqueous Solvation of Several Fluorocarbons: A Test of the Bond Potential of Mean Force Correction.
108. W. L. Jorgensen and T. B. Nguyen, J. Comput. Chem., 14, 195 (1993). Monte Carlo Simulations of the Hydration of Substituted Benzenes with OPLS Potential Functions.
109. P.-Y. Morgantini and P. A. Kollman, J. Am. Chem. Soc., 117, 6057 (1995). Solvation Free Energies of Amides and Amines: Disagreement Between Free Energy Calculations and Experiment.
110. Y. Ding, D. N. Bernardo, K. Krogh-Jespersen, and R. M. Levy, J. Phys. Chem., 99, 11575 (1995). Solvation Free Energies of Small Amides and Amines from Molecular Dynamics/ Free Energy Perturbation Simulations Using Pairwise Additive and Many-Body Polarizable Potentials.
111. E. C. Meng, J. W. Caldwell, and P. A. Kollman, J. Phys. Chem., 100, 2367 (1996). Investigating the Anomalous Solvation Free Energies of Amines with a Polarizable Potential.
112. J. W. Storer, D. J. Geisen, C. J. Cramer, and D. G. Truhlar, J. Comput.-Aided Mol. Des., 9, 87 (1995). Class IV Charge Models: A New Semiempirical Approach in Quantum Chemistry.
113. T. Z. M. Demi, T. C. Beutler, W. F. van Gunsteren, and F. Diederich, J. Phys. Chem., 100, 4256 (1996). Computation of Gibbs Free Energies of Hydration for Simple Aromatic Molecules: A Comparative Study Using Monte Carlo and Molecular Dynamics Computer Simulation Techniques.
114. J. L. Miller and P. A. Kollman, J. Phys. Chem., 100, 8587 (1996). Solvation Free Energies of the Nucleic Acid Bases.
115. K. M. Merz Jr. and P. A. Kollman, J. Am. Chem. Soc., 111, 5649 (1989). Free Energy Perturbation Simulations of the Inhibition of Thermolysin: Prediction of the Free Energy of Binding of a New Inhibitor.
116. I. Ghosh and O. Edholm, Biophys. Chem., 50, 237 (1994). Molecular Dynamics Study of the Binding of Phenylalanine Stereoisomers to Thermolysin.
117. B. G. Rao and U. C. Singh J. Am. Chem. Soc., 113, 6735 (1991). Studies on the Binding of Pepstatin and Its Derivatives to Rhizopus Pepsin by Quantum Methanics, Molecular Mechanics, and Free Energy Perturbation Methods.
118. M. R. Reddy, unpublished work, 1999. Calculation of Relative Solvation and Binding Free Energies of Inhibitors to Rhizopus Pepsin.
119. C. F. Wong and J. A. McCammon, J. Am. Chem. Soc., 108, 3830 (1986). Dynamics and Design of Enzymes and Inhibitors.
120. J. W. Essex, D. L. Severance, J. Tirado-Rives, and W. L. Jorgensen, J. Phys. Chem. B, 101, 9663 (1997). Monte Carlo Simulations for Proteins: Binding Affinities for Trypsin-Benzamidine Complexes Via Free-Energy Perturbations.
121. A. Melo and M. J. Ramos J. Peptide Res., 50, 382 (1997). The Nature of Trypsin-Pancreatic Trypsin Inhibitor Binding: Free Energy Calculation of Tyr39 → Phe39 Mutation in Trypsin.
122. S. Miyamoto and P. A. Kollman, Proc. Natl. Acad. Sci. USA, 90, 8402 (1993). What Determines the Strength of Noncovalent Association of Ligands to Proteins in Aqueous Solution?
123. B. Lesyng and E. F. Meyer, Biopolymers, 30, 773 (1990). Thermodynamic Cycle-Perturbation Study of the Binding of Trifluoroacetyl Dipeptide Anilide Inhibitors with Porcine Pancreatic Elastase.
124. J. W. Caldwell, D. A. Agard, and P. A. Kollman, Proteins, 10, 140 (1991). Free Energy Calculations on Binding and Catalysis by α-Lytic Protease: The Role of Substrate Size in the P1 Pocket.
125. S. N. Rao, U. C. Singh, P. A. Bash, and P. A. Kollman, Nature, 328, 551 (1987). Free Energy Perturbation Calculations on Binding and Catalysis After Mutating Asn 155 in Subtilisin.
126. N. Mizushima, D. Spellmeyer, S. Hirono, D. Pearlman, and P. A. Kollman, J. Biol. Chem., 266, 11801 (1991). Free Energy Perturbation Calculations on Binding and Catalysis After Mutating Threonine 220 in Subtilisin.
127. C. X. Wang, Y. Y. Shi, F. Zhou, and L. Wang, Proteins, 15, 5 (1993). Thermodynamic Integration Calculations of Binding Free Energy Difference for Gly-169 Mutation in Subtilisin BPN.
128. D. M. Ferguson, R. J. Radmer, and P. A. Kollman, J. Med. Chem., 34, 2654 (1991). Determination of the Relative Binding Free Energies of Peptide Inhibitors to the HIV-1 Protease.
129. B. G. Rao, R. F. Tilton, and U. C. Singh, J. Am. Chem. Soc., 114, 4447 (1992). Free Energy Perturbation Studies on Inhibitor Binding to HIV-1 Proteinase.
130. X. Chen and A. Tropsha, J. Med. Chem., 38, 42 (1995). Relative Binding Free Energies of Peptide Inhibitors of HIV-1 Protease: The Influence of the Active Site Protonation State.
131. B. G. Rao and M. A. Murcko, Protein Eng., 9, 767 (1996). Free Energy Perturbation Studies on Binding of A-74704 and Its Diester Analog to HIV-1 Protease.
132. P. Cieplak and P. A. Kollman, J. Comput.-Aided Mol. Des., 7, 291 (1993). Peptide Mimetics as Enzyme Inhibitors: Use of Free Energy Perturbation Calculations to Evaluate Isosteric Replacement for Amide Bonds in a Potent HIV Protease Inhibitor.
133. B. G. Rao and M. A. Murcko, J. Comput. Chem., 15, 1241 (1994). Reversed Stereochemical Preference in Binding of Ro 31-8959 to HIV-1 Proteinase: A Free Energy Perturbation Analysis.
134. B. G. Rao, C. T. Baker, J. T. Court, D. D. Deininger, J. P. Griffith, E. E. Kim, J. L. Kim, B. Li, S. Pazhanisamy, F. G. Salituro, W. C. Schairer, and R. D. Tung, in Rational Drug Design: Novel Methodology and Practical Applications, ACS Symposium Series 719, A. L. Parrill and M. R. Reddy, Eds., Oxford University Press, Washington, DC, 1999, pp. 185-197. Structure-Based Design of Novel Conformationally Restricted HIV Protease Inhibitors.
135. A. Tropsha and J. Hermans, Protein Eng., 5, 29 (1992). Application of Free Energy Simulations to the Binding of a Transition-State-Analogue Inhibitor to HIV Protease.
136. T. J. Marrone, T. P. Straatsma, J. M. Briggs, D. K. Wilson, F. A. Quiocho, and J. A. McCammon, J. Med. Chem., 39, 277 (1996). Theoretical Study of Inhibition of Adenosine Deaminase by (8R)-Coformycin and (8R)-Deoxycoformycin.
137. K. M. Merz Jr., M. A. Murcko, and P. A. Kollman, J. Am. Chem. Soc., 113, 4484 (1991). Inhibition of Carbonic Anhydrase.
138. K. A. Rossi, K. M. Merz Jr., G. M. Smith, and J. J. Baldwin, J. Med. Chem., 38, 2061 (1995). Application of the Free Energy Perturbation Method to Human Carbonic Anhydrase II Inhibitors.
139. G. Rastelli, B. Thomas, P. A. Kollman, and D. V. Santi, J. Am. Chem. Soc., 117, 7213 (1995). Insight into the Specificity of Thymidylate Synthase from Molecular Dynamics and Free Energy Perturbation Calculations.
140. M. R. Reddy and E. Villafranca, unpublished work, 1999. Calculation of Relative Binding Free Energies for Methotrexate to Three Mutants of Thymidylate Synthase.
141. S. H. Fleishman and C. L. Brooks III, Proteins, 7, 52 (1990). Protein-Drug Interactions: Characterization of Inhibitor Binding in Complexes of DHFR with Trimethoprim and Related Derivatives.
142. J. J. McDonald and C. L. Brooks III, J. Am. Chem. Soc., 113, 2295 (1991). Theoretical Approach to Drug Design. 2. Relative Thermodynamics of Inhibitor Binding by Chicken Dihydrofolate Reductase to Ethyl Derivatives of Trimethoprim Substituted at 3′-, 4′-, and 5′-Positions.
143. P. L. Cummins and J. E. Gready, Proteins, 15, 426 (1993). Novel Mechanism-Based Substructures of Dihydrofolate Reductase and the Thermodynamics of Ligand Binding: A Comparison of Theory and Experiment for 8-Methylpterin and 6,8-Dimethylpterin.
144. P. L. Cummins and J. E. Gready, J. Comput.-Aid. Mol. Des., 7, 535 (1993). Computer-Aided Drug Design: A Free Energy Perturbation Study on the Binding of Methyl-Substituted Pterins and N5-Deazapterins to Dihydrofolate Reductase.
145. J. T. Bolin, D. J. Filman, D. A. Matthews, R. C. Hamlin, and J. Kraut, J. Biol. Chem., 257, 13650 (1982). Dihydrofolate Reductase from Lactobacillus casei: X-Ray Structure of the Enzyme Methotrexate.NADPH Complex.
146. M. R. Reddy and M. D. Erion, J. Med. Chem., submitted for publication. Calculation of Relative Solvation and Binding Free Energy of FBPase Inhibitors: Using FEP Method.
147. M. R. Reddy and E. Villafranca, unpublished work, 1999. FEP Calculations on Binding Affinities or Ras Inhibitors.
148. 1 Using Molecular Dynamics/ Free Energy Perturbation Approaches.
149. T. Simonson and A. T. Brunger, Biochemistry, 31, 8661 (1992). Thermodynamics of Protein-Peptide Interactions in the Ribonuclease-S System Studied by Molecular Dynamics and Free Energy Calculations.
150. Y. Komeiji, M. Uebayasi, J.-i. Someya, and I. Yamato, Protein Eng., 5, 759 (1992). Free Energy Perturbation Study on a Trp-Binding Mutant (Ser88 → Cys) of the trp-Repressor.
151. T. Fox, T. S. Scanlan, and P. A. Kollman, J. Am. Chem. Soc., 119, 11571 (1997). Ligand Binding in the Catalytic Antibody 17E8: A Free Energy Perturbation Calculation Study.
152. D. A. Pearlman and P. R. Connelly, J. Mol. Biol., 248, 696 (1995). Determination of the Differential Effects of Hydrogen Bonding and Water Release on the Binding of FK506 to Native and Tyr82→Phe82 FKBP-12 Proteins Using Free Energy Simulations.
153. P. R. Connelly, R. A. Aldape, F. J. Bruzzese, S. P. Chambers, M. J. Fitzgibbon, M. A. Fleming, S. Itoh, D. J. Livingston, M. A. Navia, J. A. Thomson, and K. P. Wilson, Proc. Natl. Acad. Sci. USA, 91, 1964 (1994). Enthalpy of Hydrogen Bond Formation in a Protein-Ligand Binding Reaction.
154. G. Liang, R. K. Schmidt, H.-A. Yu, D. A. Cumming, and J. W. Brady, J. Phys. Chem., 2528, 100 (1996). Free Energy Simulation Studies of the Binding Specificity of Mannose-Binding Protein.
155. S. B. Singh, Ajay, D. E. Wemmer, and P. A. Kollman, Proc. Natl. Acad. Sci. USA, 91, 7673 (1994). Relative Binding Affinities of Distamycin and Its Analog to d(CGCAAGT-TGGC).d(GCCAACTTGCG): Comparison of Simulation Results with Experiment.
156. F. A. L. Anet, J. Krane, J. Dale, K. Daasvatn, and P. O. Kristiansen, Acta Chem. Scand., 27, 3395 (1973). The Conformation of 1,4,7,10-Tetraoxacyclododecane and its 1:1 Lithium Salt Complexes.
157. R. M. Izatt, D. P. Nelson, J. H. Rytting, B. L. Haymore, and J. J. Christensen, J. Am. Chem. Soc., 93, 1619 (1971). A Calorimetric Study of the Interaction in Aqueous Solution of Several Uni- and Bivalent Metal Ions with the Cyclic Polyether Dicyclohexyl-18-crown-6 at 10, 25, and 40°.
158. + Complex in Water: A Molecular Dynamics Simulation.
159. P. D. J. Grootenhuis and P. A. Kollman, J. Am. Chem. Soc., 111, 2152 (1989). Molecular Mechanics and Dynamics Studies of Crown Ether-Cation Interactions: Free Energy Calculations on the Cation Selectivity of Dibenzo-18-crown-6 and Dibenzo-30-crown-10.
160. +, and 18-Crown-6 in Methanol.
161. M. H. Mazor, J. A. McCammon, and T. P. Lybrand, J. Am. Chem. Soc., 112, 4411 (1990). Molecular Recognition in Nonaqueous Solvents. 2. Structural and Thermodynamic Analysis of Cationic Selectivity of 18-Crown-6 in Methanol.
162. Y. Sun and P. A. Kollman, J. Chem. Phys., 97, 5108 (1992). Determination of Solvation Free Energy Using Molecular Dynamics with Solute Cartesian Mapping: An Application to the Solvation of 18-Crown-6.
163. P. Cieplak, D. A. Pearlman, and P. A. Kollman, J. Chem. Phys., 101, 627 (1994). Walking on the Free Energy Hypersurface of the 18-Crown-6 Ion System Using Free Energy Derivatives.
164. + Complexation with 18-Crown-6 and Pentaglyme.
165. J. Wang and P. A. Kollman, J. Am. Chem. Soc., 120, 11106 (1998). Alkali Cation Extraction by 18-Crown-6 and Its Derivatives: A Free Energy Perturbation Study.
166. + ⊂222 Cryptates in Water and in Methanol.
167. L. Troxler and G. Wipff, J. Am. Chem. Soc., 116, 1468 (1994). Conformation and Dynamics of 18-Crown-6, Cryptand 222, and Their Cation Complexes in Acetonitrile Studied by Molecular Dynamics Simulations.
168. J. Åqvist, J. Phys. Chem., 94, 8021 (1990). Ion-Water Interaction Potentials Derived from Free Energy Perturbation Simulations.
169. B. G. Cox, J. Garcia-Rosas, and H. Schneider, J. Am. Chem. Soc., 103, 1384 (1981). Solvent Dependence of the Stability of Cryptate Complexes.
170. A. F. Danil-De-Namor and L. Ghouseeini, J. Chem. Soc., Faraday Trans., 81, 781 (1985). Enthalpies and Entropies of Complexation of Cryptand 222 and Metal Ions in Propylene Carbonate and Acetonitrile.
171. R. D. Boss and A. I. Popov, Inorg. Chem., 25, 1747 (1986). Competitive NMR Study of the Complexation of Several Cations with 18-Crown-6,1,10-diaza-18-crown-6, and Cryptand-2, 2, 2 in Nonaqueous Solutions.
172. I. Tabushi, Y.-i. Kiyosuke, T. Sugimoto, and K. Yamamura, J. Am. Chem. Soc., 100, 916 (1978). Approach to the Aspects of Driving Force of Inclusion by α-Cyclodextrin.
173. R. J. Clarke, J. H. Coates, and S. F. Lincoln, Adv. Carbohydr. Chem. Biochem., 46, 205 (1988). Inclusion Complexes of the Cyclomalto-Oligosaccharides (Cyclodextrins).
174. A. E. Mark, S. P. van Helden, P. E. Smith, L. H. M. Janssen, and W. F. van Gunsteren, J. Am. Chem. Soc., 116, 6293 (1994). Convergence Properties of Free Energy Calculations: α-Cyclodextrin Complexes as a Case Study.
175. B. C. Pressman, E. J. Harris, W. S. Jagger, and J. H. Johnson, Proc. Natl. Acad. Sci. USA, 58, 1949 (1967). Antibiotic-Mediated Transport of Alkali Ions Across Lipid Barriers.
176. P. J. Henderson, J. D. McGivan, and J. B. Chappell, Biochem. J., 111, 521 (1969). The Action of Certain Antibiotics on Mitochondrial, Erythrocyte and Artificial Phospholipid Membranes: The Role of Induced Proton Permeability.
177. S. C. Kinsky, Annu. Rev. Pharmacol., 10, 119 (1970). Antibiotic Interaction with Model Membranes.
178. B. C. Pressman, Fed. Proc., 32, 1696 (1973). Properties of Ionophores with Broad Range Cation Selectivity.
179. M. T. Burger, A. Armstrong, F. Guarnieri, D. Q. McDonald, and W. C. Still, J. Am. Chem. Soc., 116, 3593 (1994). Free Energy Calculations in Molecular Design: Predictions by Theory and Reality by Experiment with Enantioselective Podand Ionophores.
180. P. D. J. Grootenhuis, P. A. Kollman, L. C. Groenen, D. N. Reinhoudt, G. J. van Hummel, F. Ugozzoli, and G. D. Andreetti, J. Am. Chem. Soc., 112, 4165 (1990). Computational Study of the Structural, Energetical, and Acid-Base Properties of Calix[4]arenes.
181. S. Miyamoto and P. A. Kollman, J. Am. Chem. Soc., 114, 3668 (1992). Molecular Dynamics Studies of Calixspherand Complexes with Alkali Metal Cations: Calculation of the Absolute and Relative Free Energies of Binding of Cations to a Calixspherand.
182. T. J. Marrone and K. M. Merz Jr., J. Am. Chem. Soc., 114, 7542 (1992). Molecular Recognition of Potassium Ion by the Naturally Occurring Antibiotic Ionophore Nonactin.
183. P. Guilbaud, A. Varnek, and G. Wipff, J. Am. Chem. Soc., 115, 8298 (1993). Molecular Dynamics Study of p-tert-Butylcalix[4]arenetetraamide and Its Complexes with Neutral and Cationic Guests: Influences of Solvation on Structures and Stabilities.
184. J. Åqvist, O. Alvarez, and G. Eisenman, J. Phys. Chem., 96, 10019 (1992). Ion-Selective Properties of a Small Ionophore in Methanol Studied by Free Energy Perturbation Simulations.
185. B. W. Matthews, Acc. Chem. Res., 21, 33 (1988). Structural Basis of the Action of Thermolysin and Related Zinc Peptidases.
186. P. A. Bash, U. C. Singh, F. K. Brown, R. Langridge, and P. A. Kollman, Science, 235, 574 (1987). Calculation of the Relative Change in Binding Free Energy of a Protein-Inhibitor Complex.
187. B. P. Morgan, J. M. Scholtz, M. D. Ballinger, I. D. Zipkin, and P. A. Bartlett, J. Am. Chem. Soc., 113, 297 (1991). Differential Binding Energy: A Detailed Evaluation of the Influence of Hydrogen-Bonding and Hydrophobic Groups on the Inhibition of Thermolysin by Phosphorus-Containing Inhibitors.
188. D. Grobelny, U. B. Goli, and R. E. Galardy, Biochemistry, 28, 4948 (1989). Binding Energetics of Phosphorus-Containing Inhibitors of Thermolysin.
189. K. Suguna, E. A. Padlan, C. W. Smith, W. D. Carlson, and D. R. Davies, Proc. Natl. Acad. Sci. USA, 84, 7009 (1987). Binding of a Reduced Peptide Inhibitor to the Aspartic Proteinase from Rhizopus Chinensis: Implications for a Mechanism of Action.
190. R. M. Stroud, Cold Spring Harb. Symp. Quant. Biol., 36, 125 (1972). The Crystal and Molecular Structure of DIP-Inhibited Bovine Trypsin at 2.7 Ångstrom Resolution.
191. W. Bode and P. Schwager, J. Mol. Biol., 98, 693 (1975). The Refined Crystal Structure of Bovine Beta-Trypsin at 1.8 Å Resolution. II. Crystallographic Refinement, Calcium Binding Site, Benzamidine Binding Site and Active Site at pH 7.0.
192. F. C. Bernstein, T. F. Koetzle, G. J. B. Williams, E. F. Meyer, M. D. Brice, J. R. Rodgers, O. Kennard, T. Shimanouchi, and M. Tasumi, J. Mol. Biol., 112, 535 (1977). The Protein Data Bank: A Computer-Based Archival File for Macromolecular Structures.
193. H. Resat, T. J. Marrone, and J. A. McCammon, Biophys. J., 72, 522 (1997). Enzyme-Inhibitor Association Thermodynamics: Explicit and Continuum Solvent Studies.
194. M. Marquait, J. Walter, J. Deisenhofer, W. Bode, and R. Huber, Acta Crystallogr. B, 39, 480 (1983). The Geometry of the Reactive Site and of the Peptide Groups in Trypsin, Trypsinogen and its Complexes with Inhibitors.
195. A. Wlodawer, J. Walter, R. Huber, and L. Sjolin, J. Mol. Biol., 180, 301 (1984). Structure of Bovine Pancreatic Trypsin Inhibitor.
196. Z. Guo and C. L. Brooks III, J. Am. Chem. Soc., 120, 1920 (1998). Rapid Screening of Binding Affinities: Application of the λ-Dynamics Method to a Trypsin-Inhibitor System.
197. J. J. Perona and C. S. Craik, J. Biol. Chem., 272, 29987 (1997). Evolutionary Divergence of Stubstrate Specificity within the Chymotrypsin-like Serine Protease Fold.
198. M. Fujinaga, A. R. Sielecki, R. J. Read, W. Ardelt, M. Laskowski, and M. N. G. James, J. Mol. Biol., 195, 397 (1987). Crystal and Molecular Structures of the Complexed of α-Chymotrypsin with Its Inhibitor Turkey Ovomucoid Third Domain at 1.8 Ångstroms Resolution.
199. D. L. Hughes, L. C. Sieker, J. Bieth, and J.-L. Dimicoli, J. Mol. Biol., 162, 645 (1982). Crystallographic Study of the Binding of a Trifluoroacetyl Dipeptide Anilide Inhibitor with Elastase.
200. G. D. Brayer, L. T. J. D. Baere, and M. N. G. James, J. Mol. Biol., 131, 743 (1979). Molecular Structure of the Lytic Protease from Myxobacter 495 at 2.8 Å Resolution.
201. T. L. Poulos, R. A. Alden, S. T. Freer, J. J. Birktoft, and J. Kraut, J. Biol. Chem., 251, 1097 (1976). Polypeptide Halomethyl Ketones Bind to Serine Proteases as Analogs of the Tetrahedral Intermediate, X-Ray Crystallographic Comparison of Lysine- and Phenylalanine-Polypeptide Chloromethyl Ketone-Inhibited Subtilisin.
202. A. Warshel, F. Sussman, and J.-K. Hwang, J. Mol. Biol., 201, 139 (1988). Evaluation of Catalytic Free Energies in Genetically Modified Proteins.
203. R. Bott, M. Ultsch, A. Kossiakoff, T. Graycar, B. Katz, and S. Power, J. Biol. Chem., 263, 7895 (1988). The Three-Dimensional Structure of Bacillus amyhliqitefaciens Subtilisin at 1.8 Ångstroms and an Analysis of the Structural Consequences of Peroxide Inactivation.
204. S. Yun-yu, A. E. Mark, W. Cun-xin, H. Fuhua, H. J. C. Berendsen, and W. F. van Gunsteren, Protein Eng., 6, 289 (1993). Can the Stability of Protein Mutants Be Predicted by Free Energy Calculations?
205. C. A. McPhalen and M. N. G. James, Biochemistry, 27, 6582 (1988). Structural Comparison of Two Serine Proteinase-Protein Inhibitor Complexes: Eglin-c-Subtilisin Carlsberg and CI-2-Subtilisin Novo.
206. J. Kraut, Annu. Rev. Biochem., 46, 331 (1977). Serine Proteases: Structure and Mechanism of Catalysis.
207. R. A. Alden, J. J. Birktoft, J. Kraut, J. D. Robertus, and C. S. Wright, Biochem. Biophys. Res. Commun., 45, 337 (1971). Atomic Coordinates for Subtilisin BPN′ (or NOVO).
208. A. L. Swain, M. M. Miller, J. Green, D. H. Rich, J. Schneider, S. B. H. Kent, and A. Wlodawer, Proc. Natl. Acad. Sci. USA, 87, 8805 (1990). X-Ray Crystallographic Structure of a Complex Between a Synthetic Protease of Human Immunodeficiency Virus 1 and a Substrate-Based Hydroxyethyl-Amine Inhibitor.
209. N. A. Roberts, J. A. Martin, D. Kinchington, A. V. Broadhurst, J. C. Craig, I. B. Duncan, S. A. Galpin, B. K. Handa, J. Kay, A. Krohn, R. W. Lambert, J. H. Merrett, J. S. Mills, K. E. B. Parkes, S. Redshaw, A. J. Ritchie, D. L. Taylor, G. I. Thomas, and P. J. Machin, Science, 248, 358 (1990). Rational Design of Peptide-Based HIV Proteinase Inhibitors.
210. D. H. Rich, C. Q. Sun, J. V. N. V. Prasad, A. Pathiasseril, M. V. Toth, G. R. Marshall, M. Clare, R. A. Mueller, and K. Houseman, J. Med. Chem., 34, 1222 (1991). Effect of Hydroxyl Group Configuration in Hydroxyethylamine Dipeptide Isosteres on HIV Protease Inhibition: Evidence for Multiple Binding Modes.
211. M. Jaskolski, A. G. Tomasselli, T. K. Sawyer, D. G. Staples, R. L. Heinrikson, J. Schneider, S. B. H. Kent, and A. Wlodawer, Biochemistry, 30, 1600 (1991). Structure at the 2.5-Ångstrom Resolution of Chemically Synthesized Human Immunodeficiency Virus Type 1 Protease Complexed with a Hydroxyethylene-Based Inhibitor.
212. 2 Symmetric Inhibitor Complexed to HIV-1 Protease.
213. 24 Substrate Cleavage Site Are Tight-Binding Inhibitors of HIV Protease.
214. A. Wlodawer, M. Miller, M. Jaskolski, B. K. Sathyanarayana, E. Baldwin, I. T. Weber, L. M. Selk, L. Clawson, J. Schneider, and S. B. H. Kent, Science, 245, 616 (1989). Conserved Folding in Retroviral Proteases: Crystal Structure of a Synthetic HIV-1 Protease.
215. E. E. Kim, B. G. Rao, D. D. Deininger, R. D. Tung, M. D. Dwyer, J. A. Thomson, S. H. Rotstein, J. Boger, M. A. Murcko, and M. A. Navia, Nat. Struct. Biol., submitted for publication. The Diffraction Data on the Crystal of the HIV-1 Proteinase - Ro 31-8959 Complex in P61 Space Group Were Collected Out to 2.3 Å and Refined to an R-Value of 0.18.
216. L. M. Hansen and P. A. Kollman, J. Comput. Chem., 11, 994 (1990). Free Energy Perturbation Calculations on Models of Active Sites: Applications to Adenosine Deaminase Inhibitors.
217. S. C. Hoops, K. W. Anderson, and K. M. Merz Jr., J. Am. Chem. Soc., 113, 8262 (1991). Force Field Design of Metalloproteins.
218. W. L. Jorgensen, Department of Chemistry, Yale University, New Haven, CT, 1991. BOSS 3.1.
219. D. K. Wilson, F. B. Rudolph, and F. A. Quiocho, Science, 252, 1278 (1991). Atomic Structure of Adenosine Deaminase Complexed with a Transition-State Analog: Understanding Catalysis and Immunodeficiency Mutations.
220. A. J. Sharff, D. K. Wilson, Z. Chang, and F. A. Quiocho, J. Mol. Biol., 226, 917 (1992). Refined 2.5 Å Structure of Murine Adenosine Deaminase at pH 6.0.
221. - Ion to the Zinc at High pH.
222. D. A. Matthews, K. Appelt, S. J. Oatley, and N. H. Xuong, J. Mol. Biol., 214, 923 (1990). Stereochemical Mechanism of Action for Thymidylate Synthase Based on the X-Ray Structure of the Covalent Inhibitory Ternary Complex with 5-Fluoro-2′-deoxyuridylate and 5,10-Methylenetetrahydrofolate.
223. D. A. Matthews, J. E. Villafranca, C. A. Janson, W. W. Smith, K. Welsh, and S. Freer, J. Mol. Biol., 214, 937 (1990). Stereochemical Mechanism of Action for Thymidylate Synthase Based on the X-Ray Structure of the Covalent Inhibitory Ternary Complex with 5-Fluoro-2′-deoxyuridylate and 5,10-Methylenetetrahydrofolate.
224. J. S. Finer-Moore, E. B. Fauman, P. G. Foster, K. M. Perry, D. V. Santi, and R. J. Stroud, J. Mol. Biol., 232, 1101 (1993). Refined Structures of Substrate-Bound and Phosphate-Bound Thymidylate Synthase from Lactobacillus casei.
225. D. Harris and G. Loew, J. Comput. Chem., 17, 273 (1996). Comparative Study of Free Energies of Solvation of Phenylimidazole Inhibitors of Cytochrome P450cam by Free Energy Simulation, AMSOL, and Poisson Boltzmann Methods.
226. C. Oefner, A. D'Arcy, and F. K. Winkler, Eur. J. Biochem., 174, 377 (1988). Crystal Structure of Human Dihydrofolate Reductase Complexed with Folate.
227. D. A. Matthews, J. T. Bolin, J. M. Burridge, D. J. Filman, K. W. Volz, B. T. Kaufman, C. R. Beddell, J. N. Champness, D. K. Stammers, and J. Kraut, J. Biol. Chem., 260, 381 (1985). Refined Crystal Structures of Escherichia Coli and Chicken Liver Dihydrofolate Reductase Containing Bound Trimethoprim.
228. J. J. McDonald and C. L. Brooks III, J. Am. Chem. Soc., 114, 2062 (1992). A Theoretical Approach to Drug Design. 3. Relative Thermodynamics of Inhibitor Binding by E. coli Dihydrofolate Reductase to Ethyl Derivatives of Trimethoprim Substituted at 3′-, 4′-, and 5′-Positions.
229. P. L. Cummins, K. Ramnarayan, U. C. Singh, and J. E. Gready, J. Am. Chem. Soc., 113, 8247 (1991). Molecular Dynamics/Free Energy Perturbation Study on the Relative Affinities of the Binding of Reduced and Oxidized NADP to Dihydrofolate Reductase.
230. E. E. Howell, J. E. Villafranca, M. S. Warren, S. J. Oatley, and J. Kraut, Science, 231, 1123 (1986). Functional Role of Aspartic Acid-27 in Dihydrofolate Reductase Revealed by Mutagenesis.
231. +, 1999.
232. + and Biopterin.
233. U. C. Singh and S. J. Benkovic, Proc. Natl. Acad. Sci. USA, 85, 9519 (1988). A Free-Energy Perturbation Study of the Binding of Methotrexate to Mutants of Dihydrofolate Reductase.
234. U. C. Singh, Proc. Natl. Acad. Sci. USA, 85, 4280 (1988). Probing the Salt Bridge in the Dihydrofolate Reductase-Methotrexate Complex by Using the Coordinate-Coupled Free-Energy Perturbation Method.
235. H. Ke, Y. Zhang, and W. N. Lipscomb, Proc. Natl. Acad. Sci. USA, 85, 4280 (1990). Crystal Structure of Fructose-1, 6-Bisphosphatase Complexed with Fructose-6-Phosphate, AMP, and Magnesium.
236. J. E. Starrett, D. R. Tortolani, M. J. Hitchcock, J. C. Martin, and M. M. Mansuri, Antiviral Res., 19, 267 (1992). Synthesis and In Vitro Evaluation of a Phosphonate Prodrug: Bis(pivaloyloxymethyl) 9-(2-Phosphonylmethoxyethyl)adenine.
237. E. F. Pai, U. Krenger, G. A. Petsko, R. S. Goody, W. Kabsch, and A. Wittinghofer, EMBO J., 9, 2351 (1990). Refined Crystal Structure of the Triphosphate Conformation of H-ras p21 at 1.35 Å Resolution: Implications for the Mechanism of GTP Hydrolysis.
238. 12′-GMP Complex at 1.9-Å Resolution.
239. 1 Using Molecular Dynamics/Free Energy Perturbation Approaches.
240. R. Varadarajan, P. Connelly, J. Sturtevant, and F. Richards, Biochemistry, 31, 1421 (1992). Heat Capacity Changes for Protein-Peptide Interactions in the Ribonuclease-S System.
241. 1 and Implications for Catalysis.
242. R.-G. Zhang, A. Joachimiak, C. L. Lawson, R. W. Schevitz, Z. Otwinowski, and P. B. Sigler, Nature, 327, 891 (1987). The Crystal Structure of Trp Aporepressor at 1.8 Ångstrom Shows How Binding Tryptophan Enhances DNA Affinity.
243. C. L. Lawson, R.-G. Zhang, R. W. Schevits, Z. Otwinowski, A. Joachimiak, and P. B. Sigler, Proteins, 3, 18 (1988). Flexibility of the DNA-Binding Domains of Trp Repressor.
244. B. Tidor, Proteins, 19, 310 (1994). Helix-Capping Interaction in 1 Cro Protein: A Free Energy Simulation Analysis.
245. W. F. Anderson, D. H. Ohlendorf, Y. Takeda, and B. W. Matthews, Nature, 290, 754 (1981). Structure of the Cro Repressor from Bacteriophage λ and Its Interaction with DNA.
246. N. Yamaotsu, I. Moriguchi, P. A. Kollman, and S. Hirono, Biochim. Biophys. Acta, 1163, 81 (1993). Molecular Dynamics Study of the Stability of Staphylococcal Nuclease Mutants: Component Analysis of the Free Energy Difference of Denaturation.
247. 2+, and the Inhibitor pdTp, Refined at 1.65 Aθ.
248. N. Yamaotsu, I. Moriguchi, and S. Hirono, Biochim. Biophys. Acta, 1203, 243 (1993). Estimation of Stabilities of Staphylococcal Nuclease Mutants (Met32 → Ala and Met32 → Leu) Using Molecular Dynamics/Free Energy Perturbation.
249. J. C. Guo, W. Huang, and T. S. Scanlan, J. Am. Chem. Soc., 116, 6062 (1994). Kinetic and Mechanistic Characterization of an Efficient Hydrolytic Antibody: Evidence for the Formation of an Acyl Intermediate.
250. G. W. Zhou, J. Guo, W. Huang, R. J. Fletterick, and T. S. Scanlan, Science, 265, 1059 (1994). Crystal Structure of a Catalytic Antibody with a Serine Protease Active Site.
251. V. Daggett, F. Brown, and P. Kollman, J. Am. Chem. Soc., 111, 8247 (1989). Free Energy Component Analysis: A Study of the Glutamic Acid 165 → Aspartic Acid 165 Mutation in Triosephosphate Isomerase.
252. D. W. Banner, A. C. Bloomer, G. A. Petsko, D. C. Phillips, C. I. Pogson, and I. A. Wilson, Nature, 255, 609 (1975). Structure of Chicken Muscle Triose Phosphate Isomerase Determined Crystallographically at 2.5 Aθ Resolution.
253. M. Orozco, J. Tirado-Rives, and W. L. Jorgensen, Biochemistry, 32, 12864 (1993). Mechanism for the Rotamase Activity of FK506 Binding Protein from Molecular Dynamics Simulations.
254. G. D. van Duyne, R. F. Standaert, S. L. Schreiber, and J. Clardy, J. Am. Chem. Soc., 113, 7433 (1991). Atomic Structure of the Rapamycin Human Immunophilin FKBP-12 Complex.
255. M. L. Lamb and W. L. Jorgensen, J. Med. Chem., 41, 3928 (1998). Investigations of Neurotrophic Inhibitors of FK506 Binding Protein Via Monte Carlo Simulations.
256. D. A. Holt, J. I. Luengo, D. S. Yamashita, H.-J. Oh, A. L. Konialian, H.-K. Yen, L. W. Rozamus, M. Brandt, M. J. Bossard, M. A. Levy, D. S. Eggleston, J. Liang, L. W. Schultz, T. J. Stout, and J. Clardy, J. Am. Chem. Soc., 115, 9925 (1993). Design, Synthesis, and Kinetic Evaluation of High-Affinity FKBP Ligands and the X-Ray Crystal Structures of Their Complexes with FKBP12.
257. J. Gao, K. Kuczera, B. Tidor, and M. Karplus, Science, 244, 1069 (1989). Hidden Thermodynamics of Mutant Proteins: A Molecular Dynamics Analysis.
258. G. Fermi, M. F. Perutz, B. Shannan, and R. Fourme, J. Mol. Biol., 175, 159 (1984). The Crystal Structure of Human Deoxyhaemoglobin at 1.74 Å Resolution.
259. B. Shaanan, J. Mol. Biol., 171, 31 (1983). Structure of Human Oxyhaemoglobin at 2.1 Å Resolution.
260. K. Kuczera, J. Gao, B. Tidor, and M. Karplus, Proc. Natl. Acad. Sci. USA, 87, 8481 (1990). Free Energy of Sickling: A Simulation Analysis.
261. E. A. Padlan and W. E. Love, J. Biol. Chem., 260, 8272 (1985). Refined Crystal Structure of Deoxyhemoglobin S. I. Restrained Least-Squares Refinement at 3.0-Å Resolution.
262. E. A. Padlan and W. E. Love, J. Biol. Chem., 260, 8280 (1985). Refined Crystal Structure of Deoxyhemoglobin S. II. Molecular Interactions in the Crystal.
263. K. Kuczera, Biopolymers, 39, 221 (1996). Free Energy Simulations of Axial Contacts in Sickle-Cell Hemoglobin.
264. F. S. Lee, Z.-T. Chu, M. B. Bolger, and A. Warshel, Protein Eng., 5, 215 (1992). Calculations of Antibody-Antigen Interactions: Microscopic and Semi-Microscopic Evaluation of the Free Energies of Binding of Phosphorylcholine Analogs to McPC603.
265. E. A. Padlan, G. Cohen, and D. R. Davies, Ann. Instit. Pasteur (Paris), 126, 271 (1985). On the Specificity of Antibody/Antigen Interactions. Phosphocholine Binding to McPC603 and the Correlation of Three-Dimensional Structure and Sequence Data.
266. W. I. Weis, K. Drickamer, and W. A. Hendrickson, Nature, 360, 127 (1992). Structure of a C-Type Mannose-Binding Protein Complexed with an Oligosaccharide.
267. L. M. Dang, K. M. Merz Jr., and P. A. Kollman, J. Am. Chem. Soc., 111, 8508 (1989). Free Energy Calculations on Protein Stability: Thr-157 → Val-157 Mutation of T4 Lysozyme.
268. T. Alber, S. Dao-pin, K. Wilson, J. A. Wozniak, S. P. Cook, and B. W. Matthews, Nature, 330, 41 (1987). Contributions of Hydrogen Bonds of Thr 157 to the Thermodynamic Stability of Phage T4 Lysozyme.
269. T. Alber and B. W. Matthews, Methods Enzymol., 154, 511 (1987). Structure and Thermal Stability of Phage T4 Lysozyme.
270. B. Tidor and M. Karplus, Biochemistry, 30, 3217 (1991). Simulation Analysis of the Stability Mutant R96H of T4 Lysozyme.
271. M. Blaber, J. D. Lindstrom, N. Gassner, J. Xu, D. W. Heinz, and B. W. Matthews, Biochemistry, 32, 11363 (1993). Energetic Cost and Structural Consequences of Burying a Hydroxyl Group Within the Core of a Protein Determined from Ala→Ser and Val→Thr Substitutions in T4 Lysozyme.
272. L. Wang, M. A. L. Eriksson, J. Pitera, and P. A. Kollman, in Rational Drug Design: Novel Methodology and Practical Applications, ACS Symposium Series 719, A. L. Parrill and M. R. Reddy, Eds., Oxford University Press, Washington, DC, 1999, pp. 37-52. New Free Energy Calculation Methods for Structure-Based Drug Design and Prediction of Protein Stability.
273. 4 Lysozyme Using a Combination of Free Energy Derivatives, PROFEC, and Free Energy Perturbation Methods.
274. G. Ravishanker, P. Auffinger, D. R. Langley, B. Jayaram, M. A. Young, and D. L. Beveridge, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., Wiley-VCH, New York, 1997, Vol. 11, pp. 317-372. Treatment of Counterions in Computer Simulations of DNA.
275. W. S. Ross and C. C. Hardin, J. Am. Chem. Soc., 116, 6070 (1994). Ion-Induced Stabilization of the G-DNA Quadruplex: Free Energy Perturbation Studies.
276. J. R. Williamson, M. K. Raghuraman, and T. R. Cech, Cell, 59, 871 (1990). Monovalent Cation-Induced Structure of Telomeric DNA: The G-Quartet Model.
277. T. J. Dwyer, B. H. Geierstanger, Y. Bathini, J. W. Lown, and D. E. Wemmer, J. Am. Chem. Soc., 114, 5911 (1992). Design and Binding of a Distamycin A Analog to d(CGCAAGTTGGC).d(GCCAACTTGCG): Synthesis, NMR Studies, and Implications for the Design of Sequence-Specific Minor Groove Binding Oligopeptides.
278. K. Appelt, R. J. Bacquet, C. A. Bartlett, C. L. J. Booth, S. T. Freer, M. A. M. Fuhry, M. R. Gehring, S. M. Herrmann, E. F. Rowland, C. A. Janson, T. R. Jones, C. C. Kan, V. Kathardekar, K. K. Lewis, G. P. Marzoni, D. A. Matthews, C. Mohr, E. W. Moomaw, C. A. Morse, S. J. Oatley, R. C. Ogden, M. R. Reddy, S. H. Reich, W. S. Schoettlin, W. W. Smith, M. D. Varney, J. E. Villafranca, R. W. Ward, S. Webber, S. E. Webber, K. M. Welsh, and J. White, J. Med. Chem., 34, 1925 (1991). Design of Enzyme Inhibitors Using Iterative Protein Crystallographic Analysis.
279. J. A. Montgomery, S. Niwas, J. D. Rose, J. A. Secrist, Y. S. Babu, C. E. Bugg, M. D. Erion, W. C. Guida, and S. E. Ealick, J. Med. Chem., 36, 55 (1993). Structure-Based Design of Inhibitors of Purine Nucleoside Phosphorylasel: 9-(Arylmethyl) Derivatives of 9-Deazaguanine.
280. M. L. Connolly, Science, 221, 709 (1983). Solvent-Accessible Surfaces of Proteins and Nucleic Acids.
281. DelPhi, BIOSYM Technologies (now part of Molecular Simulations, Inc.), San Diego, CA, 1991.
282. P. A. Goodford, J. Med. Chem., 28, 849 (1985). A Computational Procedure for Determining Energetically Favourable Binding Sites on Biologically Important Macromolecules.
283. I. D. Kuntz, Science, 257, 1078 (1992). Structure-Based Strategies for Drug Design and Discovery.
284. H. J. Böhm, J. Comput.-Aided Mol. Des., 6, 61 (1992). The Computer Program LUDI: A New Method for the De Novo Design of Enzyme Inhibitors.
285. D. K. Gehlhaar, K. E. Moerder, D. Zichi, C. J. Sherman, R. C. Ogden, and S. T. Freer, J. Med. Chem., 38, 466 (1995). De Novo Design of Enzyme Inhibitors by Monte Carlo Ligand Generation.
286. D. R. Westhead, D. E. Clark, D. Frenkel, J. Li, C. W. Murray, B. Robson, and B. Waszkowycz, J. Comput.-Aided Mol. Des., 9, 139 (1995). PRO-LIGAND: An Approach to De Novo Molecular Design. 3. A Genetic Algorithm for Structure Refinement.
287. M. A. Murcko, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., Wiley-VCH, New York, 1997, Vol. 11, pp. 1-66. Recent Advances in Ligand Design Methods.
288. D. E. Clark, C. W. Murray, and J. Li, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., Wiley-VCH, New York, 1997, Vol. 11, pp. 67-125. Current Issues in De Novo Molecular Design.
289. R. S. DeWitte and E. I. Shakhnovich, in Rational Drug Design: Novel Methodology and Practical Applications, ACS Symposium Series 719, A. L. Parrill and M. R. Reddy, Eds., Oxford University Press, Washington, DC, 1999, pp. 70-86. SmoG: A Ligand Design Method Based on Knowledge-Based Parameterization of a Solvent Reorganization Model.
290. T. I. Oprea and C. L. Waller, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., Wiley-VCH, New York, 1997, Vol. II, pp. 127-182. Theoretical and Practical Aspects of Three-Dimensional Structure-Activity Relationships. G. Greco, E. Novellino, and Y. C. Martin, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., Wiley-VCH, New York, 1997, Vol. 11, pp. 183-240. Approaches to Three-Dimensional Quantitative Structure-Activity Relationships.
291. T. I. Oprea and C. L. Waller, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., Wiley-VCH, New York, 1997, Vol. II, pp. 127-182. Theoretical and Practical Aspects of Three-Dimensional Structure-Activity Relationships. G. Greco, E. Novellino, and Y. C. Martin, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., Wiley-VCH, New York, 1997, Vol. 11, pp. 183-240. Approaches to Three-Dimensional Quantitative Structure-Activity Relationships.
292. D. A. Thorner, P. Willen, P. M. Wright, and R. Taylor, J. Comput.-Aided Mol. Des., 11, 163 (1997). Similarity Searching in Files of Three-Dimensional Chemical Structures: Representation and Searching of Molecular Electrostatic Potentials Using Field-Graphs.
293. D. K. Agrafiotis, J.Chem. Inf. Comput. Sci., 37, 841 (1997). Stochastic Algorithms for Maximizing Molecular Diversity.
294. R. D. Brown and Y. C. Martin, J. Med. Chem., 40, 2304 (1997). Designing Combinatorial Library Mixtures Using a Genetic Algorithm.
295. W. A. Warr, J. Chem. Inf. Comput. Sci., 37, 134 (1997). Combinatorial Chemistry and Molecular Diversity. An Overview.
296. E. J. Martin, D. C. Spellmeyer, R. E. Critchlow Jr., and J. M. Blaney, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., VCH Publishers, New York, 1997, Vol. 10, pp. 75-100. Does Combinatorial Chemistry Obviate Computer-Aided Drug Design?
297. R. A. Lewis, S. D. Pickett, and D. E. Clark, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., VCH-Wiley, New York, 2000, Vol. 16, pp. 1-51. Computer-Aided Molecular Diversity Analysis and Combinatorial Library Design.
298. K. Holloway, J. M. Wai, T. A. Halgren, P. M. Fitzgerald, J. P. Vacca, B. D. Dorsey, R. B. Levin, W. J. Thompson, J. L. Chen, J. S. deSolms, N. Gaffin, A. K. Ghosh, E. A. Giuliani, S. L. Graham, J. P. Guare, R. W. Hungate, T. A. Lyle, W. M. Sanders, T. J. Tucker, M. Wiggins, C. M. Wiscount, O. W. Woltersdorf, S. D. Young, P. L. Darke, and J. A. Zugay, J. Med. Chem., 38, 305 (1995). A Priori Prediction of Activity for HIV-1 Protease Inhibitors Employing Energy Minimization in the Active Site.
299. I. D. Kurtz, E. C. Meng, and B. K. Shoichet, Acc. Chem. Res., 27, 117 (1994). Structure-Based Molecular Design.
300. R. S. Bohacek and C. McMartin, J. Med. Chem., 35, 1671 (1992). Definition and Display of Steric, Hydrophobic, and Hydrogen-Bonding Properties of Ligand Binding Sites in Proteins Using Lee and Richards Accessible Surface: Validation of a High-Resolution Graphical Tool for Drug Design.
301. M. R. Reddy and M. D. Erion, J. Enzyme Inhibitors, 14, 1 (1998). Structure-Based Drug Design Approaches for Predicting Binding Affinities of HPV1 Protease Inhibitors.
302. J. R. Damewood, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., VCH Publishers, New York, 1996, Vol. 9, pp. 1-79. Peptide Mimetic Design with the Aid of Computational Chemistry.
303. M. J. S. Dewar, E. G. Zoebisch, E. F. Healy, and J. J. P. Stewart, J. Am. Chem. Soc., 107, 3902 (1985). AMI: A New General Purpose Quantum Mechanical Molecular Model.
304. M. Miller, J. Schneider, B. K. Sathyanarayana, M. V. Selk, S. B. H. Kent, and A. Wlodawer, Science, 246, 1149 (1989). Structure of Complex of Synthetic HIV-1 Protease with a Substrate-Based Inhibitor at 2.3 Å Resolution.
305. K. Appelt, Drug Discuss Des., 1, 23 (1993). Crystal Structures of HIV-1 Protease Inhibitor Complexes: Prospects.
306. M. D. Varney, K. Appelt, V. Kalish, M. R. Reddy, J. Tatlock, C. L. Palmer, W. H. Romines, B. W. Wu, and L. Musick, J. Med. Chem., 37, 2274 (1994). Crystal-Structure-Based Design and Synthesis of Novel C-Terminal Inhibitors of HIV Protease.
307. S. J. Weiner, P. A. Kollman, D. A. Case, U. C. Singh, C. Ghio, G. Alagona, S. Profeta, and P. K. Weiner, J. Am. Chem. Soc., 106, 765 (1984). A New Force Field for Molecular Mechanical Simulation of Nucleic Acids and Proteins.
308. L. E. Chirlian and M. M. Francl, J. Comput. Chem., 8, 894 (1987). Atomic Charges Derived from Electrostatic Potentials: A Detailed Study.
309. M. J. Frisch, M. Head-Gordon, H. B. Schlegel, K. Raghavachari, J. S. Binkley, C. Gonzalez, D. J. DeFrees, D. J. Fox, R. J. Whiteside, R. Seeger, C. F. Melius, J. Baker, R. Martin, L. R. Kahn, J. J. P. Stewart, E. M. Fluder, S. Topiol, and J. A. Pople, Gaussian, Inc, Pittsburgh, PA, 1988. Gaussian 88.
310. L. Verlet, Phys. Rev., 159, 98 (1967). Computer "Experiments" on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules.