Combined molecular mechanical and continuum solvent approach (MM-PBSA/GBSA) to predict ligand binding
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MM-PBSA and MM-GBSA, which are based on molecular dynamics simulations, offer an alternative route for computing the binding free energies of protein-protein systems including coiled-coil complexes.
“Methods such as MM-PBSA and MM-GBSA,46,47 which are based on molecular dynamics (MD) simulations, offer an alternative route for computing the binding free energies of protein–protein systems48−50 including coiled-coil complexes.42,51,52”
From Assessment of the Topology and Oligomerisation States of Coiled Coils Using Metadynamics with Conformational Restraints (2025) · cites this paper as [47]
Cites
Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems
Darden, T., York, D., & Pedersen, L. (1993) · The Journal of Chemical Physics · doi:10.1063/1.464397 · Cited by 29,588 · see citing works
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
Brooks, B., Bruccoleri, R., Olafson, B. D., States, D., Swaminathan, S., & Karplus, M. (1983) · Journal of Computational Chemistry · doi:10.1002/jcc.540040211 · Cited by 13,736 · see citing works
A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules
Cornell, W. D., Cieplak, P., Bayly, C. I., Gould, I. R., Merz, K. M., Ferguson, D. M., Spellmeyer, D. C., Fox, T., Caldwell, J. W., & Kollman, P. A. (1995) · Journal of the American Chemical Society · doi:10.1021/ja00124a002 · Cited by 13,111 · see citing works
Self-citationKlamt, A., & Schüürmann, G. (1993) · Journal of the Chemical Society Perkin Transactions 2 · doi:10.1039/p29930000799 · Cited by 9,449 · see citing works
Bayly, C. I., Cieplak, P., Cornell, W. D., & Kollman, P. A. (1993) · The Journal of Physical Chemistry · doi:10.1021/j100142a004 · Cited by 8,152 · see citing works
Self-citationTomasi, J., & Persico, M. (1994) · Chemical Reviews · doi:10.1021/cr00031a013 · Cited by 5,544 · see citing works
Electric Moments of Molecules in Liquids
Onsager, L. (1936) · Journal of the American Chemical Society · doi:10.1021/ja01299a050 · Cited by 5,350 · see citing works
Semianalytical treatment of solvation for molecular mechanics and dynamics
Still, W. C., Tempczyk, A., Hawley, R. C., & Hendrickson, T. F. (1990) · Journal of the American Chemical Society · doi:10.1021/ja00172a038 · Cited by 3,653 · see citing works
Classical Electrostatics in Biology and Chemistry
Honig, B. H., & Nicholls, A. O. (1995) · Science · doi:10.1126/science.7761829 · Cited by 2,883 · see citing works
Miertuš, S., & Tomasi, J. (1982) · Chemical Physics · doi:10.1016/0301-0104(82)85072-6 · Cited by 2,480 · see citing works
Accurate Calculation of Hydration Free Energies Using Macroscopic Solvent Models
Sitkoff, D. F., Sharp, K. A., & Honig, B. H. (1994) · The Journal of Physical Chemistry · doi:10.1021/j100058a043 · Cited by 2,160 · see citing works
Free energy calculations: Applications to chemical and biochemical phenomena
Kollman, P. A. (1993) · Chemical Reviews · doi:10.1021/cr00023a004 · Cited by 2,101 · see citing works
Self-citationMolecular Modelling: Principles and Applications
Leach, A. R. (1996) · Cited by 1,944 · see citing works
Solvation energy in protein folding and binding
Eisenberg, D., & McLachlan, A. (1986) · Nature · doi:10.1038/319199a0 · Cited by 1,775 · see citing works
Continuum Solvent Studies of the Stability of DNA, RNA, and Phosphoramidate−DNA Helices
Srinivasan, J., Cheatham, T. E., Cieplak, P., Kollman, P. A., & Case, D. A. (1998) · Journal of the American Chemical Society · doi:10.1021/ja981844+ · Cited by 1,634 · see citing works
Self-citationKirkwood, J. G. (1934) · The Journal of Chemical Physics · doi:10.1063/1.1749489 · Cited by 1,529 · see citing works
High-Resolution Epitope Mapping of hGH-Receptor Interactions by Alanine-Scanning Mutagenesis
Cunningham, B. C., & Wells, J. A. (1989) · Science · doi:10.1126/science.2471267 · Cited by 1,361 · see citing works
Nicholls, A. O., & Honig, B. H. (1991) · Journal of Computational Chemistry · doi:10.1002/jcc.540120405 · Cited by 1,272 · see citing works
Solvent effects. 1. The mediation of electrostatic effects by solvents
Wong, M. W., Frisch, M. J., & Wiberg, K. B. (1991) · Journal of the American Chemical Society · doi:10.1021/ja00013a010 · Cited by 974 · see citing works
Calculation of the electric potential in the active site cleft due to α-helix dipoles
Warwicker, J., & WATSON, H. C. (1982) · Journal of Molecular Biology · doi:10.1016/0022-2836(82)90505-8 · Cited by 927 · see citing works
Method for estimating the configurational entropy of macromolecules
Karplus, M., & Kushick, J. N. (1981) · Macromolecules · doi:10.1021/ma50003a019 · Cited by 869 · see citing works
Madura, J. D., Briggs, J. M., Wade, R. C., Davis, M. E., Luty, B. A., Ilin, A., Antosiewicz, J. M., Gilson, M. K., Bagheri, B., Scott, R., et al. (1995) · Computer Physics Communications · doi:10.1016/0010-4655(95)00043-f · Cited by 808 · see citing works
Theory of Protein Titration Curves. I. General Equations for Impenetrable Spheres
Tanford, C., & Kirkwood, J. G. (1957) · Journal of the American Chemical Society · doi:10.1021/ja01577a001 · Cited by 799 · see citing works
Massova, I., & Kollman, P. A. (1999) · Journal of the American Chemical Society · doi:10.1021/ja990935j · Cited by 778 · see citing works
Self-citationKlapper, I., Hagstrom, R., Fine, R., Sharp, K. A., & Honig, B. H. (1986) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.340010109 · Cited by 757 · see citing works
Gao, J. (1996) · Accounts of Chemical Research · doi:10.1021/ar950140r · Cited by 519 · see citing works
A quantum chemical approach to dielectric solvent effects in molecular liquids
Rivail, J., & Rinaldi, D. (1976) · Chemical Physics · doi:10.1016/0301-0104(76)87050-4 · Cited by 357 · see citing works
AM1-SM2 and PM3-SM3 parameterized SCF solvation models for free energies in aqueous solution
Cramer, C. J., & Truhlar, D. G. (1992) · Journal of Computer-Aided Molecular Design · doi:10.1007/bf00126219 · Cited by 330 · see citing works
Clackson, T., Ultsch, M. H., Wells, J. A., & de Vos, A. M. (1998) · Journal of Molecular Biology · doi:10.1006/jmbi.1998.1669 · Cited by 278 · see citing works
Calculations of electrostatic energies in proteins
Russell, S. T., & Warshel, A. (1985) · Journal of Molecular Biology · doi:10.1016/0022-2836(85)90411-5 · Cited by 270 · see citing works
Jayaram, B., Sprous, D. G., & Beveridge, D. L. (1998) · The Journal of Physical Chemistry B · doi:10.1021/jp982007x · Cited by 258 · see citing works
Molecular characterization of the hdm2-p53 interaction 1 1Edited by J. Karn
Böttger, A., Böttger, V., Garcı́a-Echeverrı́a, C., Chêne, P., Hochkeppel, H. K., Sampson, W. R., Ang, K. H., Howard, S. F., Picksley, S. M., & Lane, D. P. (1997) · Journal of Molecular Biology · doi:10.1006/jmbi.1997.1078 · Cited by 251 · see citing works
Molecular dynamics and free-energy calculations applied to affinity maturation in antibody 48G7
Chong, L. T., Duan, Y., Wang, L., Massova, I., & Kollman, P. A. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.25.14330 · Cited by 250 · see citing works
Self-citationLevy, R., & Gallicchio, E. (1998) · Annual review of physical chemistry (Print) · doi:10.1146/annurev.physchem.49.1.531 · Cited by 220 · see citing works
Inclusion of Solvation in Ligand Binding Free Energy Calculations Using the Generalized-Born Model
Zou, X., Yaxiong, & Kuntz, I. D. (1999) · Journal of the American Chemical Society · doi:10.1021/ja984102p · Cited by 214 · see citing works
You, T. J., & Bashford, D. (1995) · Biophysical Journal · doi:10.1016/s0006-3495(95)80042-1 · Cited by 197 · see citing works
A Hybrid QM−MM Potential Employing Hartree−Fock or Density Functional Methods in the Quantum Region
Lyne, P. D., Hodošček, M., & Karplus, M. (1999) · The Journal of Physical Chemistry A · doi:10.1021/jp982115j · Cited by 160 · see citing works
Incorporating Solvation Effects into Density Functional Electronic Structure Calculations
Chen, J. L., Noodleman, L., Case, D. A., & Bashford, D. (1994) · The Journal of Physical Chemistry · doi:10.1021/j100094a013 · Cited by 160 · see citing works
Modeling Solvent in Biomolecular Systems
Smith, P. E., & Pettitt, B. M. (1994) · The Journal of Physical Chemistry · doi:10.1021/j100090a002 · Cited by 145 · see citing works
Constanciel, R., & Contreras, R. R. (1984) · Theoretical Chemistry Accounts · doi:10.1007/bf02427575 · Cited by 135 · see citing works
Sharp, K. A. (1991) · Journal of Computational Chemistry · doi:10.1002/jcc.540120407 · Cited by 127 · see citing works
Quantum mechanical calculations on biological systems
Friesner, R. A., & Beachy, M. D. (1998) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(98)80048-1 · Cited by 120 · see citing works
Including Side Chain Flexibility in Continuum Electrostatic Calculations of Protein Titration
Beroza, P., & Case, D. A. (1996) · The Journal of Physical Chemistry · doi:10.1021/jp9623709 · Cited by 117 · see citing works
Imaging polysaccharides by atomic force microscopy
Kirby, A. R., Gunning, A. P., & Morris, V. J. (1998) · Biopolymers · doi:10.1002/(sici)1097-0282(199603)38:3 · Cited by 107 · see citing works
Gogonea, V., & Merz, K. M. (1999) · The Journal of Physical Chemistry A · doi:10.1021/jp990266w · Cited by 99 · see citing works
Stanton, R. V., Peräkylä, M., Bakowies, D., & Kollman, P. A. (1998) · Journal of the American Chemical Society · doi:10.1021/ja972723x · Cited by 96 · see citing works
Self-citationMolecular Mechanics in Biology: From Structure to Function, Taking Account of Solvation
A, W. F. V. G., Luque, F. J., Timms, D., & Torda, A. E. (1994) · Annual Review of Biophysics and Biomolecular Structure · doi:10.1146/annurev.bb.23.060194.004215 · Cited by 91 · see citing works
Holst, M., Kozack, R. E., Saied, F., & Subramaniam, S. (1994) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.340180304 · Cited by 91 · see citing works
Optimization of Gaussian surface calculations and extension to solvent-accessible surface areas
Weiser, J., Shenkin, P. S., & Still, W. C. (1999) · Journal of Computational Chemistry · doi:10.1002/(sici)1096-987x(199905)20:7 · Cited by 76 · see citing works
Strain-Induced Bond Localization. The Heteroatom Case
Stanger, A. (1998) · Journal of the American Chemical Society · doi:10.1021/ja9819662 · Cited by 65 · see citing works
Radmer, R. J., & Kollman, P. A. (1998) · Journal of Computer-Aided Molecular Design · doi:10.1023/a:1007905722422 · Cited by 47 · see citing works
Self-citationWlodek, S. T., Antosiewicz, J. M., & McCammon, J. A. (1997) · Protein Science · doi:10.1002/pro.5560060213 · Cited by 44 · see citing works
Zhu, T., Li, J., Liotard, D., Cramer, C. J., & Truhlar, D. G. (1999) · The Journal of Chemical Physics · doi:10.1063/1.478447 · Cited by 41 · see citing works
Glennon, T. M., & Warshel, A. (1998) · Journal of the American Chemical Society · doi:10.1021/ja981594x · Cited by 40 · see citing works
Flagged first, then by citations
1 of the 55 references couldn’t be matched to a known paper.
Cited by
Sorted by citations
MMPBSA.py : An Efficient Program for End-State Free Energy Calculations
Miller, B. R., McGee, T. D., Swails, J., Homeyer, N., Gohlke, H., & Roitberg, A. E. (2012) · Journal of Chemical Theory and Computation · doi:10.1021/ct300418h · Cited by 4,664 · see citing works
gmx_MMPBSA: A New Tool to Perform End-State Free Energy Calculations with GROMACS
Tresanco, M. S. V., Valdés-Tresanco, M. E., Valiente, P. A., & Moreno, E. (2021) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.1c00645 · Cited by 3,468 · see citing works
Wang, E., Sun, H., Wang, J., Wang, Z., Liu, H., Zhang, J. Z. H., & Hou, T. (2019) · Chemical Reviews · doi:10.1021/acs.chemrev.9b00055 · Cited by 2,266 · see citing works
Gohlke, H., Kiel, C., & Case, D. (2003) · Journal of Molecular Biology · doi:10.1016/s0022-2836(03)00610-7 · Cited by 1,087 · see citing works
Wang, R., Lai, L., & Wang, S. (2002) · Journal of Computer-Aided Molecular Design · doi:10.1023/a:1016357811882 · Cited by 1,185 · see citing works
Converging free energy estimates: MM‐PB(GB)SA studies on the protein–protein complex Ras–Raf
Gohlke, H., & Case, D. (2004) · Journal of Computational Chemistry · doi:10.1002/jcc.10379 · Cited by 836 · see citing works
A fast and high-quality charge model for the next generation general AMBER force field
He, X., Man, V. H., Yang, W. Y., Lee, T., & Wang, J. (2020) · The Journal of Chemical Physics · doi:10.1063/5.0019056 · Cited by 808 · see citing works
Combining docking and molecular dynamic simulations in drug design
Alonso, H., Bliznyuk, A. A., & Gready, J. E. (2006) · Medicinal Research Reviews · doi:10.1002/med.20067 · Cited by 767 · see citing works
Calculation of absolute protein–ligand binding free energy from computer simulations
Woo, H.-J., & Roux, B. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0409005102 · Cited by 661 · see citing works
Comparative Assessment of Scoring Functions on a Diverse Test Set
Cheng, T., Li, X., Li, Y., Liu, Z., & Wang, R. (2009) · Journal of Chemical Information and Modeling · doi:10.1021/ci9000053 · Cited by 514 · see citing works
Duan, L.-L., Liu, X., & Zhang, J. (2016) · Journal of the American Chemical Society · doi:10.1021/jacs.6b02682 · Cited by 417 · see citing works
Wang, J., Deng, Y., & Roux, B. (2006) · Biophysical Journal · doi:10.1529/biophysj.106.084301 · Cited by 355 · see citing works
Greenidge, P. A., Krämer, C., Mozziconacci, J., & Wolf, R. M. (2012) · Journal of Chemical Information and Modeling · doi:10.1021/ci300425v · Cited by 336 · see citing works
Wagoner, J. A., & Baker, N. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0600118103 · Cited by 310 · see citing works
Computational alanine scanning of the 1:1 human growth hormone–receptor complex
Huo, S., Massova, I., & Kollman, P. A. (2001) · Journal of Computational Chemistry · doi:10.1002/jcc.1153 · Cited by 305 · see citing works
Self-citationDSX: A Knowledge-Based Scoring Function for the Assessment of Protein–Ligand Complexes
Neudert, G., & Klebe, G. (2011) · Journal of Chemical Information and Modeling · doi:10.1021/ci200274q · Cited by 264 · see citing works
Michel, J., & Essex, J. (2010) · J. Comput. Aided Mol. Des. · doi:10.1007/s10822-010-9363-3 · Cited by 254 · see citing works
A Guide to In Silico Drug Design
Chang, Y., Hawkins, B. A., Du, J. J., Groundwater, P. W., Hibbs, D. E., & Lai, F. (2022) · Pharmaceutics · doi:10.3390/pharmaceutics15010049 · Cited by 280 · see citing works
Singh, N., & Warshel, A. (2010) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.22687 · Cited by 229 · see citing works
Poisson–Boltzmann Methods for Biomolecular Electrostatics
Baker, N. (2004) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/s0076-6879(04)83005-2 · Cited by 224 · see citing works
Wang, R., Lu, Y., Fang, X., & Wang, S. (2004) · Journal of Chemical Information and Computer Sciences · doi:10.1021/ci049733j · Cited by 224 · see citing works
Molecular mechanical study of halogen bonding in drug discovery
Ibrahim, M. A. A. (2011) · Journal of Computational Chemistry · doi:10.1002/jcc.21836 · Cited by 223 · see citing works
Ligand binding to protein-binding pockets with wet and dry regions
Wang, L., Berne, B. J., & Friesner, R. A. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1016793108 · Cited by 214 · see citing works
Computer Simulation of Protein−Protein Interactions
Elcock, A. H., Sept, D., & McCammon, J. A. (2001) · The Journal of Physical Chemistry B · doi:10.1021/jp003602d · Cited by 214 · see citing works
Zoete, V., Meuwly, M., & Karplus, M. (2005) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.20528 · Cited by 212 · see citing works
Li, X., Xu, X. J., Wang, J., Yu, H., Wang, X., Yang, H., Xu, H., Tang, S., Li, Y., Yang, L., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0043918 · Cited by 189 · see citing works
Biomolecular electrostatics and solvation: a computational perspective
Ren, P. Y., Chun, J., Thomas, D., Schnieders, M. J., Marucho, M., Zhang, J., & Baker, N. (2012) · Quarterly Reviews of Biophysics · doi:10.1017/s003358351200011x · Cited by 183 · see citing works
Statistical potentials and scoring functions applied to protein–ligand binding
Gohlke, H., & Klebe, G. (2001) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(00)00195-0 · Cited by 181 · see citing works
Binding affinity in drug design: experimental and computational techniques
Kairys, V., Baranauskienė, L., Kazlauskiene, M., Matulis, D., & Kazlauskas, E. (2019) · Expert Opinion on Drug Discovery · doi:10.1080/17460441.2019.1623202 · Cited by 184 · see citing works
Rizzo, R. C., Aynechi, T., Case, D. A., & Kuntz, I. D. (2005) · Journal of Chemical Theory and Computation · doi:10.1021/ct050097l · Cited by 176 · see citing works
Mechanism of homodimeric cytokine receptor activation and dysregulation by oncogenic mutations
Wilmes, S., Hafer, M., Vuorio, J., Tucker, J. A., Winkelmann, H., Löchte, S., Stanly, T. A., Prieto, K. D. P., Poojari, C., Sharma, V., et al. (2020) · Science · doi:10.1126/science.aaw3242 · Cited by 175 · see citing works
Huang, K., Luo, S., Cong, Y., Zhong, S., Zhang, J. Z. H., & Duan, L. (2020) · Nanoscale · doi:10.1039/c9nr10638c · Cited by 162 · see citing works
Reyes, C. M., & Kollman, P. A. (2000) · Journal of Molecular Biology · doi:10.1006/jmbi.2000.3629 · Cited by 162 · see citing works
Self-citationWeng, G., Wang, E., Chen, F., Sun, H., Wang, Z., & Hou, T. (2019) · Physical Chemistry Chemical Physics · doi:10.1039/c9cp01674k · Cited by 157 · see citing works
Exploring the role of receptor flexibility in structure-based drug discovery
Feixas, F., Lindert, S., Sinko, W., & McCammon, J. A. (2014) · Biophysical Chemistry · doi:10.1016/j.bpc.2013.10.007 · Cited by 156 · see citing works
Laraia, L., McKenzie, G. J., Spring, D. R., Venkitaraman, A. R., & Huggins, D. J. (2015) · Chemistry & Biology · doi:10.1016/j.chembiol.2015.04.019 · Cited by 152 · see citing works
Dalal, V., Dhankhar, P., Singh, V., Singh, V., Rakhaminov, G., Golemi, D., & Kumar, P. (2021) · The Protein Journal · doi:10.1007/s10930-020-09953-6 · Cited by 151 · see citing works
Xue, W., Wang, P., Tu, G., Yang, F., Zheng, G., Li, X., Li, X., Chen, Y., Yao, X., & Zhu, F. (2018) · Physical Chemistry Chemical Physics · doi:10.1039/c7cp07869b · Cited by 150 · see citing works
An MM/3D-RISM Approach for Ligand Binding Affinities
Genheden, S., Luchko, T., Gusarov, S., Kovalenko, A., & Ryde, U. (2010) · The Journal of Physical Chemistry B · doi:10.1021/jp101461s · Cited by 148 · see citing works
Molecular Basis for Drug Resistance in HIV-1 Protease
Ali, A., Bandaranayake, R. M., Cai, Y., King, N. M., Kolli, M., Mittal, S., Foulkes-Murzycki, J. E., Nalam, M. N. L., Nalivaika, E. A., Özen, A., et al. (2010) · Viruses · doi:10.3390/v2112509 · Cited by 146 · see citing works
Self-Binding Peptides: Folding or Binding?
Yang, C., Zhang, S., He, P., Wang, C., Huang, J. H., & Zhou, P. (2015) · Journal of Chemical Information and Modeling · doi:10.1021/ci500522v · Cited by 144 · see citing works
Amaro, R. E., Cheng, X., Ivanov, I. N., Xu, D., & McCammon, J. A. (2009) · Journal of the American Chemical Society · doi:10.1021/ja8085643 · Cited by 134 · see citing works
In silico drug discovery of major metabolites from spices as SARS-CoV-2 main protease inhibitors
Ibrahim, M. A. A., Abdelrahman, A. H. M., Hussien, T. A., Badr, E. A. A., Mohamed, T. A., El-Seedi, H. R., Paré, P. W., Efferth, T., & Hegazy, M. F. (2020) · Computers in Biology and Medicine · doi:10.1016/j.compbiomed.2020.104046 · Cited by 132 · see citing works
Automatic parameterization of force field by systematic search and genetic algorithms
Wang, J., & Kollman, P. A. (2001) · Journal of Computational Chemistry · doi:10.1002/jcc.1079 · Cited by 132 · see citing works
Self-citationLi, L., Wang, Q., Zhang, Y., Niu, Y., Yao, X., & Liu, H. (2015) · PLoS ONE · doi:10.1371/journal.pone.0120330 · Cited by 129 · see citing works
A two-step binding mechanism for the self-binding peptide recognition of target domains
Yang, C., Zhang, S., Bai, Z., Hou, S., Wu, D., Huang, J. H., & Zhou, P. (2016) · Molecular BioSystems · doi:10.1039/c5mb00800j · Cited by 129 · see citing works
Wang, J., & Hou, T. (2012) · Journal of Chemical Information and Modeling · doi:10.1021/ci300064d · Cited by 128 · see citing works
Understanding Kinase Selectivity Through Energetic Analysis of Binding Site Waters
Robinson, D. D., Sherman, W., & Farid, R. (2010) · ChemMedChem · doi:10.1002/cmdc.200900501 · Cited by 125 · see citing works
Rahman, M. M., Saha, T., Islam, K. J., Suman, R. H., Biswas, S., Rahat, E. U., Hossen, M. R., Islam, R., Hossain, M. N., Mamun, A. A., et al. (2020) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2020.1794974 · Cited by 124 · see citing works
He, X., Liu, S., Lee, T., Ji, B., Man, V. H., York, D. M., & Wang, J. (2020) · ACS Omega · doi:10.1021/acsomega.9b04233 · Cited by 123 · see citing works
Wang, E., Weng, G., Sun, H., Du, H., Zhu, F., Chen, F., Wang, Z., & Hou, T. (2019) · Physical Chemistry Chemical Physics · doi:10.1039/c9cp04096j · Cited by 122 · see citing works
Solvation Model Based on Weighted Solvent Accessible Surface Area
Wang, J., Wang, W., Huo, S., Lee, M. R., & Kollman, P. A. (2001) · The Journal of Physical Chemistry B · doi:10.1021/jp0102318 · Cited by 120 · see citing works
Self-citationInteraction entropy for protein-protein binding
Sun, Z., Yan, Y. N., Yang, M., & Zhang, J. Z. H. (2017) · The Journal of Chemical Physics · doi:10.1063/1.4978893 · Cited by 117 · see citing works
Computational Alanine Scanning with Interaction Entropy for Protein–Ligand Binding Free Energies
Liu, X., Peng, L., Zhou, Y., Zhang, Y., & Zhang, J. Z. H. (2018) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.7b01295 · Cited by 120 · see citing works
Systematic Quantum Mechanical Region Determination in QM/MM Simulation
Karelina, M., & Kulik, H. J. (2017) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.6b01049 · Cited by 114 · see citing works
Parallelization of Molecular Docking: A Review
Dong, D., Xu, Z., Zhong, W., & Peng, S. (2018) · Current Topics in Medicinal Chemistry · doi:10.2174/1568026618666180821145215 · Cited by 114 · see citing works
Mena‐Ulecia, K., Tiznado, W., & Caballero, J. (2015) · PLoS ONE · doi:10.1371/journal.pone.0142774 · Cited by 109 · see citing works
Baştuğ, T., Chen, P., Patra, S. M., & Serdar Kuyucak, B. (2008) · The Journal of Chemical Physics · doi:10.1063/1.2904461 · Cited by 107 · see citing works
Emerging Methods for Ensemble-Based Virtual Screening
Amaro, R. E., & Li, W. W. (2010) · Current Topics in Medicinal Chemistry · doi:10.2174/156802610790232279 · Cited by 106 · see citing works
Ahmad, S., Raza, S., Uddin, R., & Azam, S. S. (2017) · Journal of Molecular Graphics and Modelling · doi:10.1016/j.jmgm.2017.07.024 · Cited by 102 · see citing works
Michel, J., Verdonk, M. L., & Essex, J. W. (2006) · Journal of Medicinal Chemistry · doi:10.1021/jm061021s · Cited by 100 · see citing works
Xue, W., Wang, P., Li, B., Li, Y., Xu, X., Yang, F., Yao, X., Chen, Y., Xu, F., & Zhu, F. (2015) · Physical Chemistry Chemical Physics · doi:10.1039/c5cp05771j · Cited by 98 · see citing works
Hayes, J. M., Skamnaki, V. T., Archontis, G., Lamprakis, C., Sarrou, I., Bischler, N., Skaltsounis, A., Zographos, S. E., & Oikonomakos, N. G. (2010) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.22890 · Cited by 96 · see citing works
Molecular dynamics simulation studies of novel β-lactamase inhibitor
Haq, F. U., Abro, A., Raza, S., Liedl, K. R., & Azam, S. S. (2017) · Journal of Molecular Graphics and Modelling · doi:10.1016/j.jmgm.2017.03.002 · Cited by 96 · see citing works
Zhang, Y., Ying, J. B., Hong, J. J., Li, F., Fu, T. T., Yang, F. Y., Zheng, G. X., Yao, X., Lou, Y., Qiu, Y., et al. (2019) · ACS Chemical Neuroscience · doi:10.1021/acschemneuro.8b00729 · Cited by 94 · see citing works
Woods, C. J., Malaisree, M., Michel, J., Long, B., McIntosh‐Smith, S., & Mulholland, A. J. (2014) · Faraday Discussions · doi:10.1039/c3fd00125c · Cited by 93 · see citing works
Predicting and Experimentally Validating Hot-Spot Residues at Protein–Protein Interfaces
Ibarra, A. Á., Bartlett, G. J., Hegedüs, Z., Dutt, S., Hóbor, F., Horner, K. A., Hetherington, K., Spence, K., Nelson, A. S., Edwards, T. A., et al. (2019) · ACS Chemical Biology · doi:10.1021/acschembio.9b00560 · Cited by 88 · see citing works
Kandeel, M. K., Abdelrahman, A. H. M., Oh‐hashi, K., Ibrahim, A., Venugopala, K. N., Morsy, M. A., & Ibrahim, M. A. A. (2020) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2020.1784291 · Cited by 89 · see citing works
Zhang, X., Wong, S., & Lightstone, F. C. (2013) · Journal of Chemical Information and Modeling · doi:10.1021/ci4005145 · Cited by 89 · see citing works
Ode, H., Neya, S., Hata, M., Sugiura, W., & Hoshino, T. (2006) · Journal of the American Chemical Society · doi:10.1021/ja060682b · Cited by 89 · see citing works
Natural-like products as potential SARS-CoV-2 Mpro inhibitors: in-silico drug discovery
Ibrahim, M. A. A., Abdeljawaad, K. A. A., Abdelrahman, A. H. M., & Hegazy, M. F. (2020) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2020.1790037 · Cited by 88 · see citing works
Xue, W., Pan, D., Yang, Y., Liu, H., & Yao, X. (2011) · Antiviral Research · doi:10.1016/j.antiviral.2011.11.007 · Cited by 88 · see citing works
Singh, R., Bhardwaj, V. K., & Purohit, R. (2020) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2020.1711809 · Cited by 86 · see citing works
Could MM-GBSA be accurate enough for calculation of absolute protein/ligand binding free energies?
Mulakala, C., & Viswanadhan, V. N. (2013) · Journal of Molecular Graphics and Modelling · doi:10.1016/j.jmgm.2013.09.005 · Cited by 84 · see citing works
Yang, C., Wang, C., Zhang, S., Huang, J. H., & Zhou, P. (2014) · Molecular Simulation · doi:10.1080/08927022.2014.929127 · Cited by 84 · see citing works
Biomolecular electrostatics using a fast multipole BEM on up to 512 gpus and a billion unknowns
Yokota, R., Bardhan, J. P., Knepley, M. G., Barba, L. A., & Hamada, T. (2011) · Computer Physics Communications · doi:10.1016/j.cpc.2011.02.013 · Cited by 82 · see citing works
Hassanzadeh, K., Pérez‐Peña, H., Dragotto, J., Buccarello, L., Iorio, F., Pieraccini, S., Sancini, G., & Feligioni, M. (2020) · ACS Chemical Neuroscience · doi:10.1021/acschemneuro.0c00373 · Cited by 84 · see citing works
Hou, T., Zhu, L., Chen, L., & Xu, X. (2002) · Journal of Chemical Information and Computer Sciences · doi:10.1021/ci025552a · Cited by 84 · see citing works
Structural Features of Copigmentation of Oenin with Different Polyphenol Copigments
Teixeira, N., Cruz, L., Brás, N. F., Mateus, N. F. D. C. B., Ramos, M. J., & de Freitas, V. A. P. (2013) · Journal of Agricultural and Food Chemistry · doi:10.1021/jf401174b · Cited by 84 · see citing works
Exploration of chlorinated thienyl chalcones: A new class of monoamine oxidase-B inhibitors
Mathew, B., Haridas, A., Uçar, G., Baysal, İ., Adeniyi, A. A., Soliman, M. E. S., Joy, M., Mathew, G. E., Lakshmanan, B., & Jayaprakash, V. (2016) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2016.05.110 · Cited by 83 · see citing works
Ouyang, D., Zhang, H., Parekh, H. S., & Smith, S. C. (2011) · Biophysical Chemistry · doi:10.1016/j.bpc.2011.06.003 · Cited by 83 · see citing works
Dong, L., Qu, X., Zhao, Y., & Wang, B. (2021) · ACS Omega · doi:10.1021/acsomega.1c04996 · Cited by 84 · see citing works
Adasme‐Carreño, F., Muñoz‐Gutierrez, C., Caballero, J., & Alzate‐Morales, J. H. (2014) · Physical Chemistry Chemical Physics · doi:10.1039/c4cp01378f · Cited by 81 · see citing works
Computational Methods for Biomolecular Electrostatics
Dong, F., Olsen, B. N., & Baker, N. (2007) · Methods in cell biology · doi:10.1016/s0091-679x(07)84026-x · Cited by 81 · see citing works
Maffucci, I., & Contini, A. (2013) · Journal of Chemical Theory and Computation · doi:10.1021/ct400045d · Cited by 81 · see citing works
Improving virtual screening results with MM/GBSA and MM/PBSA rescoring
Sahakyan, H. (2021) · Journal of Computer-Aided Molecular Design · doi:10.1007/s10822-021-00389-3 · Cited by 80 · see citing works
Optimized Radii for Poisson−Boltzmann Calculations with the AMBER Force Field
Swanson, J. M. J., Adcock, S. A., & McCammon, J. A. (2005) · Journal of Chemical Theory and Computation · doi:10.1021/ct049834o · Cited by 79 · see citing works
Quantitative Prediction of Fold Resistance for Inhibitors of EGFR
Balius, T. E., & Rizzo, R. C. (2009) · Biochemistry · doi:10.1021/bi900729a · Cited by 78 · see citing works
Rakib, A., Nain, Z., Sami, S. A., Mahmud, S., Islam, M. A., Ahmed, S., Siddiqui, A. B. F., Babu, S. M. O. F., Hossain, P., Shahriar, A., et al. (2021) · Briefings in Bioinformatics · doi:10.1093/bib/bbab045 · Cited by 77 · see citing works
Pearlstein, R. A., Hu, Q., Zhou, J., Yowe, D. L., Levell, J. R., Dale, B., Kaushik, V. K., Daniels, D. S., Hanrahan, S., Sherman, W., et al. (2010) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.22767 · Cited by 77 · see citing works
Role of Desolvation in Thermodynamics and Kinetics of Ligand Binding to a Kinase
Mondal, J., Friesner, R. A., & Berne, B. J. (2014) · Journal of Chemical Theory and Computation · doi:10.1021/ct500584n · Cited by 77 · see citing works
Francés‐Monerris, A., Hognon, C., Miclot, T., García‐Iriepa, C., Iriepa, I., Terenzi, A., Grandemange, S., Barone, G., Marazzi, M., & Monari, A. (2020) · Journal of Proteome Research · doi:10.1021/acs.jproteome.0c00779 · Cited by 70 · see citing works
Practical Considerations in Virtual Screening and Molecular Docking
Berry, M. J., Fielding, B. C., & Gamieldien, J. (2015) · Elsevier eBooks · doi:10.1016/b978-0-12-802508-6.00027-2 · Cited by 74 · see citing works
Flexible receptor docking for drug discovery
Wong, C. F. (2015) · Expert Opinion on Drug Discovery · doi:10.1517/17460441.2015.1078308 · Cited by 75 · see citing works
Xue, W., Jin, X., Ning, L., Wang, M., Liu, H., & Yao, X. (2012) · Journal of Chemical Information and Modeling · doi:10.1021/ci300541c · Cited by 75 · see citing works
Xu, D., Newhouse, E. I., Amaro, R. E., Pao, H. C., Cheng, L. S., Markwick, P. R. L., McCammon, J. A., Li, W. W., & ARZBERGER, P. W. (2009) · Journal of Molecular Biology · doi:10.1016/j.jmb.2009.01.040 · Cited by 74 · see citing works
A Computational Investigation of Allostery in the Catabolite Activator Protein
Li, L., Uversky, V. N., Dunker, A. K., & Meroueh, S. O. (2007) · Journal of the American Chemical Society · doi:10.1021/ja076046a · Cited by 71 · see citing works
Singh, R., Bhardwaj, V. K., Das, P., & Purohit, R. (2019) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2019.1696709 · Cited by 71 · see citing works
Ahmad, E., Rabbani, G., Zaidi, N., Khan, M. A., Qadeer, A., Ishtikhar, M., Singh, S. P., & Khan, R. H. (2012) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2012.706081 · Cited by 71 · see citing works
Identification of naturally originated molecules as γ-aminobutyric acid receptor antagonist
Sharma, J., Bhardwaj, V. K., Das, P., & Purohit, R. (2020) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2020.1720818 · Cited by 70 · see citing works
- Authors
- Massova, I., & Kollman, P. A.
- Affiliations
- University of California, San Francisco (US)
- Venue
- Perspectives in Drug Discovery and Design
- Published
- 2000-06
- Volume
- 18
- Issue
- 1
- Pages
- 113-135
- ISSN
- 0928-2866 (ISSN-L)
- 1573-9023
- OpenAlex
- W1549357029
- Cited by
- 1,015
- References
- 55
- Citations by year
- 2026: 58 · 2025: 85 · 2024: 64 · 2023: 85 · 2022: 67 · 2021: 83 · 2020: 57 · 2019: 46 · 2018: 48 · 2017: 47 · 2016: 46 · 2015: 39 · 2014: 45 · 2013: 36 · 2012: 34
- FWCI
- 10.76
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- Locations
- Perspectives in Drug Discovery and Design (publishedVersion)
- Funders
- National Institute for Health and Care Research
- National Institutes of Health
- Topics
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
- Physical Sciences › Physics and Astronomy › Atomic and Molecular Physics, and Optics › Advanced Chemical Physics Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Keywords
- MM-PBSA, ligand binding prediction, binding free energy, solvent effects, solvation energy, scanning mutagenesis, molecular dynamics, high-throughput screening, binding affinity ranking
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