Combined molecular mechanical and continuum solvent approach (MM-PBSA/GBSA) to predict ligand binding

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 29,638

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

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

COSMO: a new approach to dielectric screening in solvents with explicit expressions for the screening energy and its gradient

Klamt, A., & Schüürmann, G. (1993) · Journal of the Chemical Society Perkin Transactions 2 · doi:10.1039/p29930000799 · Cited by 9,449

A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model

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

Molecular Interactions in Solution: An Overview of Methods Based on Continuous Distributions of the Solvent

Tomasi, J., & Persico, M. (1994) · Chemical Reviews · doi:10.1021/cr00031a013 · Cited by 5,530

Electric Moments of Molecules in Liquids

Onsager, L. (1936) · Journal of the American Chemical Society · doi:10.1021/ja01299a050 · Cited by 5,350

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

Classical Electrostatics in Biology and Chemistry

Honig, B. H., & Nicholls, A. O. (1995) · Science · doi:10.1126/science.7761829 · Cited by 2,891

Approximate evaluations of the electrostatic free energy and internal energy changes in solution processes

Miertuš, S., & Tomasi, J. (1982) · Chemical Physics · doi:10.1016/0301-0104(82)85072-6 · Cited by 2,480

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

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

End-Point Binding Free Energy Calculation with MM/PBSA and MM/GBSA: Strategies and Applications in Drug Design

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 2,341

Insights into Protein–Protein Binding by Binding Free Energy Calculation and Free Energy Decomposition for the Ras–Raf and Ras–RalGDS Complexes

Gohlke, H., Kiel, C., & Case, D. A. (2003) · Journal of Molecular Biology · doi:10.1016/s0022-2836(03)00610-7 · Cited by 1,205

Further development and validation of empirical scoring functions for structure-based binding affinity prediction

Wang, R., Lai, L., & Wang, S. (2002) · Journal of Computer-Aided Molecular Design · doi:10.1023/a:1016357811882 · Cited by 1,185

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

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 824

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 784

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

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 525

Interaction Entropy: A New Paradigm for Highly Efficient and Reliable Computation of Protein-Ligand Binding Free Energy.

Duan, L.-L., Liu, X., & Zhang, J. (2016) · Journal of the American Chemical Society · doi:10.1021/jacs.6b02682 · Cited by 417

Absolute Binding Free Energy Calculations Using Molecular Dynamics Simulations with Restraining Potentials

Wang, J., Deng, Y., & Roux, B. (2006) · Biophysical Journal · doi:10.1529/biophysj.106.084301 · Cited by 355

MM/GBSA Binding Energy Prediction on the PDBbind Data Set: Successes, Failures, and Directions for Further Improvement

Greenidge, P. A., Krämer, C., Mozziconacci, J., & Wolf, R. M. (2012) · Journal of Chemical Information and Modeling · doi:10.1021/ci300425v · Cited by 336

Assessing implicit models for nonpolar mean solvation forces: The importance of dispersion and volume terms

Wagoner, J. A., & Baker, N. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0600118103 · Cited by 310

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

DSX: 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 272

Prediction of protein–ligand binding affinity by free energy simulations: assumptions, pitfalls and expectations

Michel, J., & Essex, J. W. (2010) · Journal of Computer-Aided Molecular Design · doi:10.1007/s10822-010-9363-3 · Cited by 266

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 296

Absolute binding free energy calculations: On the accuracy of computational scoring of protein–ligand interactions

Singh, N., & Warshel, A. (2010) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.22687 · Cited by 229

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

An Extensive Test of 14 Scoring Functions Using the PDBbind Refined Set of 800 Protein−Ligand Complexes

Wang, R., Lu, Y., Fang, X., & Wang, S. (2004) · Journal of Chemical Information and Computer Sciences · doi:10.1021/ci049733j · Cited by 228

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

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

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 213

Study of the insulin dimerization: Binding free energy calculations and per‐residue free energy decomposition

Zoete, V., Meuwly, M., & Karplus, M. (2005) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.20528 · Cited by 212

A System-Level Investigation into the Mechanisms of Chinese Traditional Medicine: Compound Danshen Formula for Cardiovascular Disease Treatment

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 188

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 188

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 184

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

Estimation of Absolute Free Energies of Hydration Using Continuum Methods: Accuracy of Partial Charge Models and Optimization of Nonpolar Contributions

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

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

An accurate free energy estimator: based on MM/PBSA combined with interaction entropy for protein–ligand binding affinity

Huang, K., Luo, S., Cong, Y., Zhong, S., Zhang, J. Z. H., & Duan, L. (2020) · Nanoscale · doi:10.1039/c9nr10638c · Cited by 163

Structure and thermodynamics of RNA-protein binding: using molecular dynamics and free energy analyses to calculate the free energies of binding and conformational change11Edited by B. Honig

Reyes, C. M., & Kollman, P. A. (2000) · Journal of Molecular Biology · doi:10.1006/jmbi.2000.3629 · Cited by 162

Assessing the performance of MM/PBSA and MM/GBSA methods. 9. Prediction reliability of binding affinities and binding poses for protein–peptide complexes

Weng, G., Wang, E., Chen, F., Sun, H., Wang, Z., & Hou, T. (2019) · Physical Chemistry Chemical Physics · doi:10.1039/c9cp01674k · Cited by 157

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

Overcoming Chemical, Biological, and Computational Challenges in the Development of Inhibitors Targeting Protein-Protein Interactions

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 154

Structure-Based Identification of Potential Drugs Against FmtA of Staphylococcus aureus: Virtual Screening, Molecular Dynamics, MM-GBSA, and QM/MM

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

Computational identification of the binding mechanism of a triple reuptake inhibitor amitifadine for the treatment of major depressive disorder

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 151

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

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

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

Characterizing Loop Dynamics and Ligand Recognition in Human- and Avian-Type Influenza Neuraminidases via Generalized Born Molecular Dynamics and End-Point Free Energy Calculations

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

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

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

The Molecular Mechanism of Bisphenol A (BPA) as an Endocrine Disruptor by Interacting with Nuclear Receptors: Insights from Molecular Dynamics (MD) Simulations

Li, L., Wang, Q., Zhang, Y., Niu, Y., Yao, X., & Liu, H. (2015) · PLoS ONE · doi:10.1371/journal.pone.0120330 · Cited by 137

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

Develop and Test a Solvent Accessible Surface Area-Based Model in Conformational Entropy Calculations

Wang, J., & Hou, T. (2012) · Journal of Chemical Information and Modeling · doi:10.1021/ci300064d · Cited by 128

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 127

Virtual screening, molecular dynamics and structure–activity relationship studies to identify potent approved drugs for Covid-19 treatment

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

Fast, Accurate, and Reliable Protocols for Routine Calculations of Protein–Ligand Binding Affinities in Drug Design Projects Using AMBER GPU-TI with ff14SB/GAFF

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 125

Assessing the performance of the MM/PBSA and MM/GBSA methods. 10. Impacts of enhanced sampling and variable dielectric model on protein–protein Interactions

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

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

Interaction 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

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

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

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 118

Study of the Differential Activity of Thrombin Inhibitors Using Docking, QSAR, Molecular Dynamics, and MM-GBSA

Mena‐Ulecia, K., Tiznado, W., & Caballero, J. (2015) · PLoS ONE · doi:10.1371/journal.pone.0142774 · Cited by 111

Potential of mean force calculations of ligand binding to ion channels from Jarzynski’s equality and umbrella sampling

Baştuğ, T., Chen, P., Patra, S. M., & Serdar Kuyucak, B. (2008) · The Journal of Chemical Physics · doi:10.1063/1.2904461 · Cited by 107

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

Binding mode analysis, dynamic simulation and binding free energy calculations of the MurF ligase from Acinetobacter baumannii

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 104

Protein-Ligand Binding Affinity Predictions by Implicit Solvent Simulations: A Tool for Lead Optimization?

Michel, J., Verdonk, M. L., & Essex, J. W. (2006) · Journal of Medicinal Chemistry · doi:10.1021/jm061021s · Cited by 100

Identification of the inhibitory mechanism of FDA approved selective serotonin reuptake inhibitors: an insight from molecular dynamics simulation study

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

Kinetics, in silico docking, molecular dynamics, and MM‐GBSA binding studies on prototype indirubins, KT5720, and staurosporine as phosphorylase kinase ATP‐binding site inhibitors: The role of water molecules examined

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 101

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

How Does Chirality Determine the Selective Inhibition of Histone Deacetylase 6? A Lesson from Trichostatin A Enantiomers Based on Molecular Dynamics

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 95

Rapid decomposition and visualisation of protein–ligand binding free energies by residue and by water

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

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 90

Repurposing of FDA-approved antivirals, antibiotics, anthelmintics, antioxidants, and cell protectives against SARS-CoV-2 papain-like protease

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 88

Toward Fully Automated High Performance Computing Drug Discovery: A Massively Parallel Virtual Screening Pipeline for Docking and Molecular Mechanics/Generalized Born Surface Area Rescoring to Improve Enrichment

Zhang, X., Wong, S., & Lightstone, F. C. (2013) · Journal of Chemical Information and Modeling · doi:10.1021/ci4005145 · Cited by 91

Computational Simulations of HIV-1 ProteasesMulti-drug Resistance Due to Nonactive Site Mutation L90M

Ode, H., Neya, S., Hata, M., Sugiura, W., & Hoshino, T. (2006) · Journal of the American Chemical Society · doi:10.1021/ja060682b · Cited by 89

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

Molecular modeling study on the resistance mechanism of HCV NS3/4A serine protease mutants R155K, A156V and D168A to TMC435

Xue, W., Pan, D., Yang, Y., Liu, H., & Yao, X. (2011) · Antiviral Research · doi:10.1016/j.antiviral.2011.11.007 · Cited by 88

Identification of a novel binding mechanism of Quinoline based molecules with lactate dehydrogenase of Plasmodium falciparum

Singh, R., Bhardwaj, V. K., & Purohit, R. (2020) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2020.1711809 · Cited by 86

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

Structural and energetic insights into the intermolecular interaction among human leukocyte antigens, clinical hypersensitive drugs and antigenic peptides

Yang, C., Wang, C., Zhang, S., Huang, J. H., & Zhou, P. (2014) · Molecular Simulation · doi:10.1080/08927022.2014.929127 · Cited by 84

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

Considerations around the SARS-CoV-2 Spike Protein with Particular Attention to COVID-19 Brain Infection and Neurological Symptoms

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 83

Mapping the Binding Site of a Large Set of Quinazoline Type EGF-R Inhibitors Using Molecular Field Analyses and Molecular Docking Studies

Hou, T., Zhu, L., Chen, L., & Xu, X. (2002) · Journal of Chemical Information and Computer Sciences · doi:10.1021/ci025552a · Cited by 84

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

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 84

The effect of pH on PAMAM dendrimer–siRNA complexation — Endosomal considerations as determined by molecular dynamics simulation

Ouyang, D., Zhang, H., Parekh, H. S., & Smith, S. C. (2011) · Biophysical Chemistry · doi:10.1016/j.bpc.2011.06.003 · Cited by 83

Prediction of Binding Free Energy of Protein–Ligand Complexes with a Hybrid Molecular Mechanics/Generalized Born Surface Area and Machine Learning Method

Dong, L., Qu, X., Zhao, Y., & Wang, B. (2021) · ACS Omega · doi:10.1021/acsomega.1c04996 · Cited by 88

Performance of the MM/GBSA scoring using a binding site hydrogen bond network-based frame selection: the protein kinase case

Adasme‐Carreño, F., Muñoz‐Gutierrez, C., Caballero, J., & Alzate‐Morales, J. H. (2014) · Physical Chemistry Chemical Physics · doi:10.1039/c4cp01378f · Cited by 80

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 82

Explicit Ligand Hydration Shells Improve the Correlation between MM-PB/GBSA Binding Energies and Experimental Activities

Maffucci, I., & Contini, A. (2013) · Journal of Chemical Theory and Computation · doi:10.1021/ct400045d · Cited by 81

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

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

Quantitative Prediction of Fold Resistance for Inhibitors of EGFR

Balius, T. E., & Rizzo, R. C. (2009) · Biochemistry · doi:10.1021/bi900729a · Cited by 78

A molecular modelling approach for identifying antiviral selenium-containing heterocyclic compounds that inhibit the main protease of SARS-CoV-2: an in silico investigation

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 79

New hypotheses about the structure–function of proprotein convertase subtilisin/kexin type 9: Analysis of the epidermal growth factor‐like repeat A docking site using WaterMap

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

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

Molecular Basis of SARS-CoV‑2 Infection and Rational Design of Potential Antiviral Agents: Modeling and Simulation Approaches

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 72

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 77

Flexible receptor docking for drug discovery

Wong, C. F. (2015) · Expert Opinion on Drug Discovery · doi:10.1517/17460441.2015.1078308 · Cited by 76

Exploring the Molecular Mechanism of Cross-Resistance to HIV-1 Integrase Strand Transfer Inhibitors by Molecular Dynamics Simulation and Residue Interaction Network Analysis

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

Distinct Glycan Topology for Avian and Human Sialopentasaccharide Receptor Analogues upon Binding Different Hemagglutinins: A Molecular Dynamics Perspective

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 75

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

Natural analogues inhibiting selective cyclin-dependent kinase protein isoforms: a computational perspective

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

Revisiting ligand-induced conformational changes in proteins: essence, advancements, implications and future challenges

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

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

Tuning the Solvation Term in the MM-PBSA/GBSA Binding Affinity Predictions

Maffucci, I. (2015) · BENTHAM SCIENCE PUBLISHERS eBooks · Cited by 1

Assessment of Computational Methods for Ligand Binding

Mikulskis, P. (2015) · Lund University Publications (Lund University)

The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities

Genheden, S., & Ryde, U. (2015) · Expert Opinion on Drug Discovery · doi:10.1517/17460441.2015.1032936 · Cited by 5,769

Case-specific performance of MM-PBSA, MM-GBSA, and SIE in virtual screening

Virtanen, S. I., Niinivehmas, S. P., & Pentikäinen, O. T. (2015) · Journal of Molecular Graphics and Modelling · doi:10.1016/j.jmgm.2015.10.012 · Cited by 68

MM-GB(PB)SA Calculations of Protein-Ligand Binding Free Energies

Hayes, J., & Archontis, G. (2012) · InTech eBooks · doi:10.5772/37107 · Cited by 142