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Caccamo C, Costa D, Pellicane G. A comprehensive study of the phase diagram of symmetrical hard-core Yukawa mixtures. J Chem Phys 1998. [DOI: 10.1063/1.477053] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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LISZI TAMASKRISTOFJANOS. Alternative Gibbs ensemble Monte Carlo implementations: application in mixtures. Mol Phys 1998. [DOI: 10.1080/002689798168024] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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153
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Marrone TJ, Resat H, Hodge CN, Chang CH, McCammon JA. Solvation studies of DMP323 and A76928 bound to HIV protease: analysis of water sites using grand canonical Monte Carlo simulations. Protein Sci 1998; 7:573-9. [PMID: 9541388 PMCID: PMC2143944 DOI: 10.1002/pro.5560070305] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We examine the water solvation of the complex of the inhibitors DMP323 and A76928 bound to HIV-1 protease through grand canonical Monte Carlo simulations, and demonstrate the ability of this method to reproduce crystal waters and effectively predict water positions not seen in the DMP323 or A76928 structures. The simulation method is useful for identifying structurally important waters that may not be resolved in the crystal structures. It can also be used to identify water positions around a putative drug candidate docked into a binding pocket. Knowledge of these water positions may be useful in designing drugs to utilize them as bridging groups or displace them in the binding pocket. In addition, the method should be useful in finding water sites in homology models of enzymes for which crystal structures are unavailable.
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Affiliation(s)
- T J Marrone
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla 92093-0365, USA
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Blas FJ, Vega LF. Prediction of Binary and Ternary Diagrams Using the Statistical Associating Fluid Theory (SAFT) Equation of State. Ind Eng Chem Res 1998. [DOI: 10.1021/ie970449+] [Citation(s) in RCA: 222] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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155
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Phase transitions in nonadditive hard disc systems: a Gibbs ensemble Monte Carlo Study. Colloid Polym Sci 1997. [DOI: 10.1007/bf01182440] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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156
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Mecke M, Winkelmann J, Fischer J. Molecular dynamics simulation of the liquid–vapor interface: The Lennard-Jones fluid. J Chem Phys 1997. [DOI: 10.1063/1.475217] [Citation(s) in RCA: 252] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Matthias Mecke
- Institut für Physikalische Chemie, Universität Halle-Wittenberg, Geusaer Str., D-06217 Merseburg, Germany
| | - Jochen Winkelmann
- Institut für Physikalische Chemie, Universität Halle-Wittenberg, Geusaer Str., D-06217 Merseburg, Germany
| | - Johann Fischer
- Institut für Land-, Umwelt-, und Energietechnik, Universität für Bodenkultur, Peter-Jordan-Strasse 82, A-1190 Wien, Austria
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157
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Zarragoicoechea GJ, Scalise OH. On the gas–gas equilibria of second kind of nonpolar fluid binary mixtures from a hard-sphere EXP-6 molecular model. J Chem Phys 1997. [DOI: 10.1063/1.474777] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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159
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Kumar SK. Computer Simulations on the Free Energies and Phase Diagrams of Asymmetrically Interacting Blends. Macromolecules 1997. [DOI: 10.1021/ma961348a] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sanat K. Kumar
- Department of Materials Science and Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802
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160
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Parsonage NG. A Grand-Canonical Ensemble Monte Carlo Study of the Effects of Change of Core Size on the Thermodynamic Properties of a Modified Lennard-Jones Fluid. MOLECULAR SIMULATION 1997. [DOI: 10.1080/08927029708024148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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161
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Gao GT, Zeng XC, Wang W. Vapor–liquid coexistence of quasi-two-dimensional Stockmayer fluids. J Chem Phys 1997. [DOI: 10.1063/1.473079] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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162
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Anta JA, Lomba E, Alvarez M, Lombardero M, Martín C. Gas−Liquid Coexistence Properties from Reference Hypernetted Chain Theory for Linear Polar Solvents. J Phys Chem B 1997. [DOI: 10.1021/jp9629708] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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163
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Lísal M, Vacek V. Direct Evaluation of Solid–Liquid Equilibria by Molecular Dynamics Using Gibbs-Duhem Integration. MOLECULAR SIMULATION 1997. [DOI: 10.1080/08927029708024137] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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164
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Mackie AD, Tavitian B, Boutin A, Fuchs AH. Vapour-Liquid Phase Equilibria Predictions of Methane–Alkane Mixtures by Monte Carlo Simulation. MOLECULAR SIMULATION 1997. [DOI: 10.1080/08927029708024135] [Citation(s) in RCA: 71] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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165
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SADUS RICHARDJ. RESEARCH NOTE Molecular simulation of the liquid-liquid equilibria of binary mixtures containing dipolar and non-polar components interacting via the Keesom potential. Mol Phys 1996. [DOI: 10.1080/002689796173589] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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166
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Cifra P, Nies E, Broersma J. Equation of State and Miscibility Behavior of Compressible Binary Lattice Polymers. A Monte Carlo Study and Comparison with Partition Function Theories. Macromolecules 1996. [DOI: 10.1021/ma960154s] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Peter Cifra
- Polymer Institute, Slovak Academy of Sciences, 842 36 Bratislava, Slovakia
| | - Erik Nies
- Eindhoven Polymer Laboratories, Faculty of Chemical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600MB Eindhoven, The Netherlands
| | - Jabik Broersma
- Eindhoven Polymer Laboratories, Faculty of Chemical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600MB Eindhoven, The Netherlands
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167
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Lísal M, Vacek V. Direct Evaluation of Vapour-Liquid Equilibria of Mixtures by Molecular Dynamics Using Gibbs-Duhem Integration. MOLECULAR SIMULATION 1996. [DOI: 10.1080/08927029608022355] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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168
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Strigari L, Rovere M, D’Aguanno B. Theory of gas–gas phase transition in rare‐gas binary mixtures. J Chem Phys 1996. [DOI: 10.1063/1.472070] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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169
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Wilding NB, Müller M, Binder K. Chain length dependence of the polymer–solvent critical point parameters. J Chem Phys 1996. [DOI: 10.1063/1.471889] [Citation(s) in RCA: 107] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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170
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McGrother SC, Jackson G. Island of vapor-liquid coexistence in dipolar hard-core systems. PHYSICAL REVIEW LETTERS 1996; 76:4183-4186. [PMID: 10061222 DOI: 10.1103/physrevlett.76.4183] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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Goldman S, Gray CG, Li W, Tomberli B, Joslin CG. Predicting Solubilities in Supercritical Fluids. ACTA ACUST UNITED AC 1996. [DOI: 10.1021/jp953286g] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- S. Goldman
- Guelph-Waterloo Program for Graduate Work in Physics, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - C. G. Gray
- Guelph-Waterloo Program for Graduate Work in Physics, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - W. Li
- Guelph-Waterloo Program for Graduate Work in Physics, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - B. Tomberli
- Guelph-Waterloo Program for Graduate Work in Physics, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - C. G. Joslin
- Guelph-Waterloo Program for Graduate Work in Physics, University of Guelph, Guelph, Ontario, Canada N1G 2W1
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Sadus RJ. Molecular simulation of the vapour-liquid equilibria of pure fluids and binary mixtures containing dipolar components: the effect of Keesom interactions. Mol Phys 1996. [DOI: 10.1080/00268979600100661] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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174
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Kotelyanskii MJ, Hentschke R. Gibbs-Ensemble Molecular Dynamics: Liquid-Gas Equilibria for Lennard-Jones Spheres and n-Hexane. MOLECULAR SIMULATION 1996. [DOI: 10.1080/08927029608024099] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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175
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Sadus RJ, Prausnitz JM. Three‐body interactions in fluids from molecular simulation: Vapor–liquid phase coexistence of argon. J Chem Phys 1996. [DOI: 10.1063/1.471172] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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176
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Lomba E, Alvarez M, Lee LL, Almarza NG. Phase stability of binary non‐additive hard‐sphere mixtures: A self‐consistent integral equation study. J Chem Phys 1996. [DOI: 10.1063/1.471229] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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177
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Lísal M, Vacek V. Direct Evaluation of Vapour-Liquid Equilibria by Molecular Dynamics using Gibbs-Duhem Integration. MOLECULAR SIMULATION 1996. [DOI: 10.1080/08927029608024092] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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178
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Monte Carlo simulation of fluid phase equilibria in pore systems: square-well fluid distributed over a bulk and a slit-pore. Chem Phys Lett 1996. [DOI: 10.1016/0009-2614(95)01433-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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179
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Resat H, Mezei M, McCammon JA. Use of the Grand Canonical Ensemble in Potential of Mean Force Calculations. ACTA ACUST UNITED AC 1996. [DOI: 10.1021/jp951496n] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- H. Resat
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093-0365, and Department of Biophysics and Physiology, Mount Sinai School of Medicine, New York, New York 10029-6574
| | - M. Mezei
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093-0365, and Department of Biophysics and Physiology, Mount Sinai School of Medicine, New York, New York 10029-6574
| | - J. A. McCammon
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093-0365, and Department of Biophysics and Physiology, Mount Sinai School of Medicine, New York, New York 10029-6574
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de Miguel E, Martín del Río E, Telo da Gama MM. Liquid–liquid phase equilibria of symmetrical mixtures by simulation in the semigrand canonical ensemble. J Chem Phys 1995. [DOI: 10.1063/1.470446] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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182
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Nezbeda I, Strnad M. Monte Carlo simulations in the vicinity of the critical point: Vapour-liquid coexistence curve. ACTA ACUST UNITED AC 1995. [DOI: 10.1007/bf01691392] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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183
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Wilding NB. Critical-point and coexistence-curve properties of the Lennard-Jones fluid: A finite-size scaling study. PHYSICAL REVIEW. E, STATISTICAL PHYSICS, PLASMAS, FLUIDS, AND RELATED INTERDISCIPLINARY TOPICS 1995; 52:602-611. [PMID: 9963461 DOI: 10.1103/physreve.52.602] [Citation(s) in RCA: 297] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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184
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Rull LF, Jackson G, Smit B. The condition of microscopic reversibility in Gibbs ensemble Monte Carlo simulations of phase equilibria. Mol Phys 1995. [DOI: 10.1080/00268979500101231] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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185
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Boda D, Liszi J, Szalai I. Dielectric constant of a Stockmayer fluid along the vapour-liquid coexistence curve. Mol Phys 1995. [DOI: 10.1080/00268979500101221] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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186
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Stevens MJ, Grest GS. Structure of soft-sphere dipolar fluids. PHYSICAL REVIEW. E, STATISTICAL PHYSICS, PLASMAS, FLUIDS, AND RELATED INTERDISCIPLINARY TOPICS 1995; 51:5962-5975. [PMID: 9963335 DOI: 10.1103/physreve.51.5962] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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187
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Patrykiejew A, Sokol/owski S, Zientarski T, Binder K. Monte Carlo study of melting and disordering in monolayer films formed on the (100) face of face centered cubic crystals. J Chem Phys 1995. [DOI: 10.1063/1.469233] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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188
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Schneider F, Marx D, Nielaba P. Gibbs-ensemble path-integral Monte Carlo simulations of a mixed quantum-classical fluid. PHYSICAL REVIEW. E, STATISTICAL PHYSICS, PLASMAS, FLUIDS, AND RELATED INTERDISCIPLINARY TOPICS 1995; 51:5162-5165. [PMID: 9963240 DOI: 10.1103/physreve.51.5162] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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189
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Kotelyanskii MJ, Hentschke R. Gibbs-ensemble molecular dynamics: Liquid-gas equilibrium in a Lennard-Jones system. PHYSICAL REVIEW. E, STATISTICAL PHYSICS, PLASMAS, FLUIDS, AND RELATED INTERDISCIPLINARY TOPICS 1995; 51:5116-5119. [PMID: 9963228 DOI: 10.1103/physreve.51.5116] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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190
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Caillol JM. A Monte Carlo study of the dielectric constant of the restricted primitive model of electrolytes on the vapor branch of the coexistence line. J Chem Phys 1995. [DOI: 10.1063/1.469275] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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191
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Boda D, Liszi J, Szalai I. An extension of the NpT plus test particle method for the determination of the vapour-liquid equilibria of pure fluids. Chem Phys Lett 1995. [DOI: 10.1016/0009-2614(95)00066-d] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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192
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Wilding NB, Müller M. Liquid–vapor asymmetry in pure fluids: A Monte Carlo simulation study. J Chem Phys 1995. [DOI: 10.1063/1.468686] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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193
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Smit B, Karaborni S, Siepmann JI. Computer simulations of vapor–liquid phase equilibria ofn‐alkanes. J Chem Phys 1995. [DOI: 10.1063/1.469563] [Citation(s) in RCA: 430] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Nakanishi K. Physical property prediction based on molecular simulation for simple model fluids. JOURNAL OF CHEMICAL ENGINEERING OF JAPAN 1995. [DOI: 10.1252/jcej.28.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Koichiro Nakanishi
- Department of Polymer Chemistry, Faculty of Engineering, Kyoto University
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Green DG, Jackson G, de Miguel E, Rull LF. Vapor–liquid and liquid–liquid phase equilibria of mixtures containing square‐well molecules by Gibbs ensemble Monte Carlo simulation. J Chem Phys 1994. [DOI: 10.1063/1.467565] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Orkoulas G, Panagiotopoulos AZ. Free energy and phase equilibria for the restricted primitive model of ionic fluids from Monte Carlo simulations. J Chem Phys 1994. [DOI: 10.1063/1.467770] [Citation(s) in RCA: 190] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Stevens MJ, Grest GS. Coexistence in dipolar fluids in a field. PHYSICAL REVIEW LETTERS 1994; 72:3686-3689. [PMID: 10056264 DOI: 10.1103/physrevlett.72.3686] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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Lomba E, Weis JJ, Almarza NG, Bresme F, Stell G. Phase transitions in a continuum model of the classical Heisenberg magnet: The ferromagnetic system. PHYSICAL REVIEW. E, STATISTICAL PHYSICS, PLASMAS, FLUIDS, AND RELATED INTERDISCIPLINARY TOPICS 1994; 49:5169-5178. [PMID: 9961841 DOI: 10.1103/physreve.49.5169] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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Lomba E, Almarza NG. Role of the interaction range in the shaping of phase diagrams in simple fluids. The hard sphere Yukawa fluid as a case study. J Chem Phys 1994. [DOI: 10.1063/1.466781] [Citation(s) in RCA: 145] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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