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Comparison of simple potential functions for simulating liquid water

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The Elements of Statistical Learning

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A smooth particle mesh Ewald method

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Development and testing of a general amber force field

Wang, J.-M., Wolf, R., Caldwell, J., Kollman, P., & Case, D. (2004) · Journal of Computational Chemistry · doi:10.1002/jcc.20035 · Cited by 18,318

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Inference from iterative simulation using multiple sequences

Gelman, A., & Rubin, D. B. (1992) · Statistical Science · doi:10.1214/ss/1177011136 · Cited by 16,627

On the limited memory BFGS method for large scale optimization

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GROMACS 3.0: a package for molecular simulation and trajectory analysis

Lindahl, E. R., Hess, B., & van der Spoel, D. (2001) · Journal of Molecular Modeling · doi:10.1007/s008940100045 · Cited by 6,953

Optimized Potential of Mean Force Calculations for Standard Binding Free Energies

Buch, I., Sadiq, S. K., & Fabritiis, G. D. (2011) · Journal of Chemical Theory and Computation · doi:10.1021/ct2000638 · Cited by 42

Sparse Sampling of Water Density Fluctuations in Interfacial Environments

Xi, E., Remsing, R. C., & Patel, A. J. (2016) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.5b01037 · Cited by 43

Comparing the Performance of Different AMBER Protein Forcefields, Partial Charge Assignments, and Water Models for Absolute Binding Free Energy Calculations

Huggins, D. J. (2022) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.1c01208 · Cited by 42

Broadening the Scope of Binding Free Energy Calculations Using a Separated Topologies Approach

Baumann, H. M., Dybeck, E. C., McClendon, C. L., Pickard, F. C., Gapsys, V., Pérez‐Benito, L., Hahn, D. F., Tresadern, G., Mathiowetz, A. M., & Mobley, D. L. (2023) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.3c00282 · Cited by 40

Substrate-Induced Conformational Changes in the S-Component ThiT from an Energy Coupling Factor Transporter

Majsnerowska, M., Hänelt, I., Wunnicke, D., Schäfer, L. V., Steinhoff, H., & Slotboom, D. J. (2013) · Structure · doi:10.1016/j.str.2013.03.007 · Cited by 40

Solvent effects on ligand binding to a serine protease

Gopal, S. M., Klumpers, F., Herrmann, C., & Schäfer, L. V. (2017) · Physical Chemistry Chemical Physics · doi:10.1039/c6cp07899k · Cited by 40

The Role of Interfacial Water in Protein–Ligand Binding: Insights from the Indirect Solvent Mediated Potential of Mean Force

Cui, D., Zhang, B. W., Matubayasi, N., & Levy, R. M. (2017) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.7b01076 · Cited by 37

Enhanced Monte Carlo Methods for Modeling Proteins Including Computation of Absolute Free Energies of Binding

de Vaca, I. C., Qian, Y., Vilseck, J. Z., Tirado-Rives, J., & Jorgensen, W. L. (2018) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.8b00031 · Cited by 35

Improved Binding Free Energy Predictions from Single-Reference Thermodynamic Integration Augmented with Hamiltonian Replica Exchange

Khavrutskii, I., & Wallqvist, A. (2011) · Journal of Chemical Theory and Computation · doi:10.1021/ct2003786 · Cited by 41

Water-Mediated Conformations of the Alanine Dipeptide as Revealed by Distributed Umbrella Sampling Simulations, Quantum Mechanics Based Calculations, and Experimental Data

Cruz, V. L., Ramos, J., & Martínez‐Salazar, J. (2011) · The Journal of Physical Chemistry B · doi:10.1021/jp2022727 · Cited by 36

Using Free Energy of Binding Calculations to Improve the Accuracy of Virtual Screening Predictions

Malmstrom, R. D., & Watowich, S. (2011) · Journal of Chemical Information and Modeling · doi:10.1021/ci200126v · Cited by 35

Calculation of absolute protein-ligand binding free energy using distributed replica sampling

Rodinger, T., Howell, P. L., & Pomès, R. (2008) · The Journal of Chemical Physics · doi:10.1063/1.2989800 · Cited by 35

Fragment-Based Computation of Binding Free Energies by Systematic Sampling

Clark, M., Meshkat, S. N., Talbot, G. T., Carnevali, P., & Wiseman, J. S. (2009) · Journal of Chemical Information and Modeling · doi:10.1021/ci900132r · Cited by 35

Calculating the sensitivity and robustness of binding free energy calculations to force field parameters

Rocklin, G., Mobley, D., & Dill, K. (2013) · Journal of Chemical Theory and Computation · doi:10.1021/ct400315q · Cited by 33

Absolute Binding Free Energies between T4 Lysozyme and 141 Small Molecules: Calculations Based on Multiple Rigid Receptor Configurations

Xie, B., Nguyen, T. H., & Minh, D. D. L. (2017) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.6b01183 · Cited by 35

Meta-Analysis Reveals That Absolute Binding Free-Energy Calculations Approach Chemical Accuracy

Fu, H., Zhou, Y.-B., Xiang, J., Shao, X., & Cai, W. (2022) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.2c00796 · Cited by 34

Exploring the free-energy landscapes of biological systems with steered molecular dynamics

Chen, L. Y. (2011) · Physical Chemistry Chemical Physics · doi:10.1039/c0cp02799e · Cited by 33

Relative Contributions of Solubility and Mobility to the Stability of Amorphous Solid Dispersions of Poorly Soluble Drugs: A Molecular Dynamics Simulation Study

Brunsteiner, M., Khinast, J., & Paudel, A. (2018) · Pharmaceutics · doi:10.3390/pharmaceutics10030101 · Cited by 33

Non-equilibrium approach for binding free energies in cyclodextrins in SAMPL7: force fields and software

Khalak, Y., Tresadern, G., de Groot, B. L., & Gapsys, V. (2020) · Journal of Computer-Aided Molecular Design · doi:10.1007/s10822-020-00359-1 · Cited by 36

Comparison of Receptor–Ligand Restraint Schemes for Alchemical Absolute Binding Free Energy Calculations

Clark, F., Robb, G. R., Cole, D. J., & Michel, J. (2023) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.3c00139 · Cited by 31

Force field parameters for S -nitrosocysteine and molecular dynamics simulations of S -nitrosated thioredoxin

Han, S. (2008) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2008.10.017 · Cited by 33

Effect of Side-Chain Structure of Rigid Polyimide Dispersant on Mechanical Properties of Single-Walled Carbon Nanotube/Cyanate Ester Composite

Yuan, W., Li, W., Mu, Y., & Chan‐Park, M. B. E. (2011) · ACS Applied Materials & Interfaces · doi:10.1021/am2002229 · Cited by 32

Exploring Conformational Change of Adenylate Kinase by Replica Exchange Molecular Dynamic Simulation

Wang, J., Peng, C., Yu, Y., Chen, Z., Xu, Z., Cai, T., Shao, Q., Shi, J., & Zhu, W. (2020) · Biophysical Journal · doi:10.1016/j.bpj.2020.01.001 · Cited by 31

Efficient free energy calculations on small molecule host‐guest systems—A combined linear interaction energy/one‐step perturbation approach

Oostenbrink, C. (2008) · Journal of Computational Chemistry · doi:10.1002/jcc.21116 · Cited by 31

Absolute Free Energy of Binding Calculations for Macrophage Migration Inhibitory Factor in Complex with a Druglike Inhibitor

Qian, Y., de Vaca, I. C., Vilseck, J. Z., Cole, D. J., Tirado‐Rives, J., & Jorgensen, W. L. (2019) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.9b07588 · Cited by 32

Adapting free energy perturbation simulations for large macrocyclic ligands: how to dissect contributions from direct binding and free ligand flexibility

Wallraven, K., Holmelin, F. L., Glas, A., Hennig, S., Frolov, A. I., & Grossmann, T. N. (2020) · Chemical Science · doi:10.1039/c9sc04705k · Cited by 30

Computation of Standard Binding Free Energies of Polar and Charged Ligands to the Glutamate Receptor GluA2

Heinzelmann, G., Chen, P., & Kuyucak, S. (2014) · The Journal of Physical Chemistry B · doi:10.1021/jp412195m · Cited by 30

The plastoquinol–plastoquinone exchange mechanism in photosystem II: insight from molecular dynamics simulations

Zobnina, V., Lambreva, M. D., Rea, G., Campi, G., Antonacci, A., Scognamiglio, V., Giardi, M. T., & Polticelli, F. (2016) · Photosynthesis Research · doi:10.1007/s11120-016-0292-4 · Cited by 29

Impact of Quadrupolar Electrostatics on Atoms Adjacent to the Sigma-Hole in Condensed-Phase Simulations

Hage, K. E., Bereau, T., Jakobsen, S., & Meuwly, M. (2016) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.6b00202 · Cited by 28

Dodecyl Maltoside Protects Membrane Proteins In Vacuo

Rouse, S. L., Marcoux, J., Robinson, C. V., & Sansom, M. S. P. (2013) · Biophysical Journal · doi:10.1016/j.bpj.2013.06.025 · Cited by 28

Absolute Organic Crystal Thermodynamics: Growth of the Asymmetric Unit into a Crystal via Alchemy

Park, J., Nessler, I., McClain, B., Macikenas, D., Baltrušaitis, J., & Schnieders, M. J. (2014) · Journal of Chemical Theory and Computation · doi:10.1021/ct500180m · Cited by 29

Exploring the role of cyclodextrins as a cholesterol scavenger: a molecular dynamics investigation of conformational changes and thermodynamics

Koli, M. G., & Fogolari, F. (2023) · Scientific Reports · doi:10.1038/s41598-023-49217-8 · Cited by 27

Computing the Relative Stabilities and the Per-Residue Components in Protein Conformational Changes

Roy, A., Pérez, A., Dill, K. A., & MacCallum, J. L. (2013) · Structure · doi:10.1016/j.str.2013.10.015 · Cited by 27

Biophysical Characterization of a Nanodisc with and without BAX: An Integrative Study Using Molecular Dynamics Simulations and Cryo-EM

López, C. A., Swift, M. F., Xu, X., Hanein, D., Volkmann, N., & Gnanakaran, S. (2019) · Structure · doi:10.1016/j.str.2019.03.013 · Cited by 26

Computing Relative Free Energies of Solvation Using Single Reference Thermodynamic Integration Augmented with Hamiltonian Replica Exchange

Khavrutskii, I. V., & Wallqvist, A. (2010) · Journal of Chemical Theory and Computation · doi:10.1021/ct1003302 · Cited by 26

Heme Binding Mechanism of Structurally Similar Iron-Regulated Surface Determinant Near Transporter Domains ofStaphylococcus aureusExhibiting Different Affinities for Heme

Moriwaki, Y., Terada, T., Caaveiro, J. M. M., Takaoka, Y., Hamachi, I., Tsumoto, K., & Shimizu, K. (2013) · Biochemistry · doi:10.1021/bi4008325 · Cited by 26

Free Energy-Based Virtual Screening and Optimization of RNase H Inhibitors of HIV-1 Reverse Transcriptase

Zhang, B., D’Erasmo, M. P., Murelli, R. P., & Gallicchio, E. (2016) · ACS Omega · doi:10.1021/acsomega.6b00123 · Cited by 27

Modeling of Arylamide Helix Mimetics in the p53 Peptide Binding Site of hDM2 Suggests Parallel and Anti-Parallel Conformations Are Both Stable

Fuller, J. C., Jackson, R. M., Edwards, T. A., Wilson, A. J., & Shirts, M. R. (2012) · PLoS ONE · doi:10.1371/journal.pone.0043253 · Cited by 24

Ligand-Receptor Affinities Computed by an Adapted Linear Interaction Model for Continuum Electrostatics and by Protein Conformational Averaging

Nunes-Alves, A., & Arantes, G. M. (2014) · Journal of Chemical Information and Modeling · doi:10.1021/ci500301s · Cited by 18

Pushing the Limits of Detection of Weak Binding Using Fragment-Based Drug Discovery: Identification of New Cyclophilin Binders

Georgiou, C., McNae, I. W., Wear, M. A., Ioannidis, H., Michel, J., & Walkinshaw, M. D. (2017) · Journal of Molecular Biology · doi:10.1016/j.jmb.2017.06.016 · Cited by 25

Sampling Conformational Changes of Bound Ligands Using Nonequilibrium Candidate Monte Carlo and Molecular Dynamics

Sasmal, S., Gill, S. C., Lim, N. M., & Mobley, D. L. (2020) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.9b01066 · Cited by 25

Lambda-ABF: Simplified, Portable, Accurate, and Cost-Effective Alchemical Free-Energy Computation

Lagardère, L., Maurin, L., Adjoua, O., Hage, K. E., Monmarché, P., Piquemal, J., & Hénin, J. (2024) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.3c01249 · Cited by 28

Energy landscapes and global thermodynamics for alanine peptides

Somani, S., & Wales, D. J. (2013) · The Journal of Chemical Physics · doi:10.1063/1.4813627 · Cited by 23

Molecular simulations of micellar aggregation of polysorbate 20 ester fractions and their interaction with N-phenyl-1-naphthylamine dye

Lapelosa, M., Patapoff, T. W., & Zarraga, I. E. (2016) · Biophysical Chemistry · doi:10.1016/j.bpc.2016.03.003 · Cited by 23

A Metadynamics-Based Protocol for the Determination of GPCR-Ligand Binding Modes

Söldner, C. A., Horn, A. H. C., & Sticht, H. (2019) · International Journal of Molecular Sciences · doi:10.3390/ijms20081970 · Cited by 23

On Computing Equilibrium Binding Constants for Protein–Protein Association in Membranes

Majumder, A., Kwon, S., & Straub, J. E. (2022) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.2c00106 · Cited by 20

Use of a Chondroitin Sulfate Isomer as an Effective and Removable Dispersant of Single‐Walled Carbon Nanotubes

Yan, L. Y., Li, W., Mesgari, S., Leong, S. S. J., Chen, Y., Loo, L. S., Mu, Y., & Chan‐Park, M. B. E. (2011) · Small · doi:10.1002/smll.201100708 · Cited by 22

A detailed computational study on binding of kinase inhibitors into β-cyclodextrin: inclusion complex formation

Mojdehi, M. F., Koli, M. G., Bolagh, M. D. O., Gardeh, M. G., & Hashemianzadeh, S. M. (2020) · Molecular Systems Design & Engineering · doi:10.1039/d0me00140f · Cited by 21

PyFepRestr: Plugin to PyMOL Molecular Graphics System for Calculating the Free Energy of Ligand‒Receptor Binding

Lashkov, A. A., Tolmachev, I. V., Eistrikh-Heller, P. A., & Rubinsky, S. V. (2021) · Crystallography Reports · doi:10.1134/s1063774521050126 · Cited by 21

Equilibrium exchange enhances the convergence rate of umbrella sampling

Neale, C., Rodinger, T., & Pomès, R. (2008) · Chemical Physics Letters · doi:10.1016/j.cplett.2008.05.099 · Cited by 21

Selectivity and Cooperativity of Modulatory Ions in a Neurotransmitter Receptor

Vijayan, R., Plested, A. J. R., Mayer, M. L., & Biggin, P. C. (2009) · Biophysical Journal · doi:10.1016/j.bpj.2008.11.039 · Cited by 22

Calculation and Visualization of Atomistic Mechanical Stresses in Nanomaterials and Biomolecules

Fenley, A. T., Muddana, H. S., & Gilson, M. K. (2014) · PLoS ONE · doi:10.1371/journal.pone.0113119 · Cited by 18

Bringing Clarity to the Prediction of Protein–Ligand Binding Free Energies via “Blurring”

Ucisik, M. N., Zheng, Z., Faver, J. C., & Merz, K. M. (2014) · Journal of Chemical Theory and Computation · doi:10.1021/ct400995c · Cited by 20

Absolute protein binding free energy simulations for ligands with multiple poses, a thermodynamic path which avoids exhaustive enumeration of the poses

Yoshitake, S., Zhang, B. W., Levy, R., & Deng, N. (2019) · Journal of Computational Chemistry · doi:10.1002/jcc.26078 · Cited by 16

Predicting the Solubility of the Sparingly Soluble Solids 1,2,4,5-Tetramethylbenzene, Phenanthrene, and Fluorene in Various Organic Solvents by Molecular Simulation

Paluch, A. S., Cryan, D. D., & Maginn, E. J. (2011) · Journal of Chemical & Engineering Data · doi:10.1021/je101251n · Cited by 20

Phosphorylation Regulates the Bound Structure of an Intrinsically Disordered Protein: The p53-TAZ2 Case

Ithuralde, R. E., & Turjanski, A. G. (2016) · PLoS ONE · doi:10.1371/journal.pone.0144284 · Cited by 19

Accurate calculation of mutational effects on the thermodynamics of inhibitor binding to p38α MAP kinase: a combined computational and experimental study

Zhu, S., Travis, S., & Elcock, A. (2013) · Journal of Chemical Theory and Computation · doi:10.1021/ct400104x · Cited by 21

The SAMPL9 host–guest blind challenge: an overview of binding free energy predictive accuracy

Amezcua, M., Setiadi, J., & Mobley, D. L. (2024) · Physical Chemistry Chemical Physics · doi:10.1039/d3cp05111k · Cited by 19

Unveiling the dynamic and thermodynamic interactions of hydrocortisone with β-cyclodextrin and its methylated derivatives through insights from molecular dynamics simulations

Gholami, R., Azizi, K., & Koli, M. G. (2024) · Scientific Reports · doi:10.1038/s41598-024-63034-7 · Cited by 18

A MOLECULAR DYNAMICS SIMULATION STUDY OF CONFORMATIONAL CHANGES AND SOLVATION OF Aβ PEPTIDE IN TRIFLUOROETHANOL AND WATER

Jalili, S., & Akhavan, M. (2009) · Journal of Theoretical and Computational Chemistry · doi:10.1142/s0219633609004769 · Cited by 18

Mechanistic Insights into the Stimulant Properties of Novel Psychoactive Substances (NPS) and Their Discrimination by the Dopamine Transporter—In Silico and In Vitro Exploration of Dissociative Diarylethylamines

Sahai, M. A., Davidson, C., Dutta, N., & Opacka‐Juffry, J. (2018) · Brain Sciences · doi:10.3390/brainsci8040063 · Cited by 18

Structure and aggregation in model tetramethylurea solutions

Gupta, R., & Patey, G. N. (2014) · The Journal of Chemical Physics · doi:10.1063/1.4892411 · Cited by 18

Symmetry-Adapted Restraints for Binding Free Energy Calculations

Ebrahimi, M., & Hénin, J. (2022) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.1c01235 · Cited by 19

Calculation of absolute free energy of binding for theophylline and its analogs to RNA aptamer using nonequilibrium work values

Tanida, Y., Ito, M., & Fujitani, H. (2007) · Chemical Physics · doi:10.1016/j.chemphys.2007.07.014 · Cited by 17

Nonbonded Force Field Parameters from Minimal Basis Iterative Stockholder Partitioning of the Molecular Electron Density Improve CB7 Host–Guest Affinity Predictions

González, D., Macaya, L., Castillo-Orellana, C., Verstraelen, T., Vogt‐Geisse, S., & Vöhringer‐Martinez, E. (2022) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.2c00316 · Cited by 16

Independent-Trajectory Thermodynamic Integration: A Practical Guide to Protein-Drug Binding Free Energy Calculations Using Distributed Computing

Lawrenz, M., Baron, R., Wang, Y., & McCammon, J. A. (2011) · Methods in molecular biology · doi:10.1007/978-1-61779-465-0_27 · Cited by 16

Calculation of binding affinities for linear alcohols to α -cyclodextrin by twin-system enveloping distribution sampling simulations

Gebhardt, J., & Hansen, N. (2016) · Fluid Phase Equilibria · doi:10.1016/j.fluid.2016.02.001 · Cited by 17

Discrimination between cyclic nucleotides in a cyclic nucleotide-gated ion channel

Pan, Y., Pohjolainen, E., Schmidpeter, P. A. M., Vaiana, A. C., Nimigean, C. M., Grubmüller, H., & Simon Scheuring, A. (2023) · Nature Structural & Molecular Biology · doi:10.1038/s41594-023-00955-3 · Cited by 15

Interactions of calmodulin with death-associated protein kinase peptides: experimental and modeling studies

Kuczera, K., & Kursula, P. (2012) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2012.674221 · Cited by 15

Role of Ligand Reorganization and Conformational Restraints on the Binding Free Energies of DAPY Non-Nucleoside Inhibitors to HIV Reverse Transcriptase

Gallicchio, E. (2012) · Computational Molecular Bioscience · doi:10.4236/cmb.2012.21002 · Cited by 15

Hydration Free Energy from Orthogonal Space Random Walk and Polarizable Force Field

Abella, J. R., Cheng, S. Y., Wang, Q., Yang, W. Y., & Ren, P. Y. (2014) · Journal of Chemical Theory and Computation · doi:10.1021/ct500202q · Cited by 16

Free Energy of Binding of a Small Molecule to an Amorphous Polymer in a Solvent

Chunsrivirot, S., & Trout, B. L. (2011) · Langmuir · doi:10.1021/la201011q · Cited by 15

Integration of Multiscale Molecular Modeling Approaches with the Design and Discovery of Fusidic Acid Derivatives

Lu, J., Ni, J., Wang, J., Liu, Z.-Y., Shang, K., & Bi, Y. (2019) · Future Medicinal Chemistry · doi:10.4155/fmc-2018-0567 · Cited by 15

Estimating the Roles of Protonation and Electronic Polarization in Absolute Binding Affinity Simulations

King, E. J., Qi, R., Li, H., Luo, R., & Aitchison, E. W. (2021) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.0c01305 · Cited by 15

Insights into Ligand–Protein Binding from Local Mechanical Response

Patel, J. S., Branduardi, D., Masetti, M., Rocchia, W., & Cavalli, A. (2011) · Journal of Chemical Theory and Computation · doi:10.1021/ct200324j · Cited by 15

Energetics of Double-Ion Occupancy in the Gramicidin A Channel

Li, Y., Andersen, O. S., & Roux, B. (2010) · The Journal of Physical Chemistry B · doi:10.1021/jp105820u · Cited by 15

Binding Energy Distribution Analysis Method: Hamiltonian Replica Exchange with Torsional Flattening for Binding Mode Prediction and Binding Free Energy Estimation

Mentes, A., Deng, N.-J., Vijayan, R., Xia, J., Gallicchio, E., & Levy, R. M. (2016) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.6b00134 · Cited by 16

Binding Free Energies of Host–Guest Systems by Nonequilibrium Alchemical Simulations with Constrained Dynamics: Illustrative Calculations and Numerical Validation

Giovannelli, E., Cioni, M., Procacci, P., Cardini, G., Pagliai, M., Volkov, V. V., & Chelli, R. (2017) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.7b00595 · Cited by 15

On Restraints in End‐Point Protein–Ligand Binding Free Energy Calculations

Menzer, W. M., Xie, B., & Minh, D. D. L. (2019) · Journal of Computational Chemistry · doi:10.1002/jcc.26119 · Cited by 17

Rapid Heme Transfer Reactions between NEAr Transporter Domains of Staphylococcus aureus: A Theoretical Study Using QM/MM and MD Simulations

Moriwaki, Y., Terada, T., Tsumoto, K., & Shimizu, K. (2015) · PLoS ONE · doi:10.1371/journal.pone.0145125 · Cited by 16

Formation and molecular dynamics simulation of inclusion complex of large‐ring cyclodextrin and 4‐terpineol

Cao, C., Deng, C., Hu, J., & Zhou, Y. (2022) · Journal of Food Science · doi:10.1111/1750-3841.16303 · Cited by 14

An amber compatible molecular mechanics force field for the anticancer drug topotecan

Chillemi, G., Coletta, A., Mancini, G., Sanna, N., & Desideri, A. (2009) · Theoretical Chemistry Accounts · doi:10.1007/s00214-009-0715-9 · Cited by 14

Detailed potential of mean force studies on host–guest systems from the SAMPL6 challenge

Song, L. F., Bansal, N., Zheng, Z., & Merz, K. M. (2018) · Journal of Computer-Aided Molecular Design · doi:10.1007/s10822-018-0153-7 · Cited by 14

Alchemical free energy calculations via metadynamics: Application to the theophylline‐RNA aptamer complex

Tanida, Y., & Matsuura, A. (2020) · Journal of Computational Chemistry · doi:10.1002/jcc.26221 · Cited by 14

Structural properties of hydroxyl-substituted alkyl benzenesulfonates at the water/vapor and water/decane interfaces

Sun, H., Xiao, H., & Liu, X. (2011) · Science China Chemistry · doi:10.1007/s11426-011-4305-z · Cited by 14

Enhanced Sampling Methods in Drug Design

Rocchia, W., Masetti, M., & Cavalli, A. (2012) · Royal Society of Chemistry eBooks · doi:10.1039/9781849735377-00273 · Cited by 15

Binding of histamine to the H1 receptor—a molecular dynamics study

Söldner, C. A., Horn, A. H. C., & Sticht, H. (2018) · Journal of Molecular Modeling · doi:10.1007/s00894-018-3873-7 · Cited by 14

PopShift: A Thermodynamically Sound Approach to Estimate Binding Free Energies by Accounting for Ligand-Induced Population Shifts from a Ligand-Free Markov State Model

Smith, L. G., Novak, B., Osato, M., Mobley, D. L., & Bowman, G. R. (2024) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.3c00870 · Cited by 15

Molecular insights into the role of a distal F240A mutation that alters CYP1A1 activity towards persistent organic pollutants

Navrátilová, V., Paloncýová, M., Berka, K., Mise, S., Haga, Y., Matsumura, C., Sakaki, T., Inui, H., & Otyepka, M. (2017) · Biochimica et Biophysica Acta (BBA) - General Subjects · doi:10.1016/j.bbagen.2017.08.002 · Cited by 13

Molecular mechanism of secreted amyloid-β precursor protein in binding and modulating GABA B R1a

Feng, M., Song, Y., Chen, S. H., Zhang, Y., & Zhou, R. (2021) · Chemical Science · doi:10.1039/d0sc06946a · Cited by 13

Theoretical studies on the interaction of modified pyrimidines and purines with purine riboswitch

Ling, B., Wang, Z., Zhang, R., Meng, X.-H., Liu, Y., Zhang, C., & Liu, C. (2009) · Journal of Molecular Graphics and Modelling · doi:10.1016/j.jmgm.2009.03.005 · Cited by 13

Kartograf: A Geometrically Accurate Atom Mapper for Hybrid-Topology Relative Free Energy Calculations

Ries, B., Alibay, I., Swenson, D. W. H., Baumann, H. M., Henry, M. M., Eastwood, J. R. B., & Gowers, R. J. (2024) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.3c01206 · Cited by 12

Optimizing Absolute Binding Free Energy Calculations for Production Usage

Wu, Z., König, G., Boresch, S., & Cossins, B. P. (2025) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.5c00861 · Cited by 13

Accelerating Convergence of Free Energy Computations with Hamiltonian Simulated Annealing of Solvent (HSAS)

Jiang, W. (2019) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.8b01147 · Cited by 12

A theoretical study on the mechanism of a superficial mutation inhibiting the enzymatic activity of CYP1A2

Ma, L., Du, Z., Lian, P., & Wei, D. (2014) · Interdisciplinary Sciences Computational Life Sciences · doi:10.1007/s12539-014-0184-2 · Cited by 11

Molecular Dynamics Free Energy Calculations to Assess the Possibility of Water Existence in Protein Nonpolar Cavities

Oikawa, M., & Yonetani, Y. (2010) · Biophysical Journal · doi:10.1016/j.bpj.2010.01.029 · Cited by 11

Prediction of Ligand Binding Affinity by the Combination of Replica-Exchange Method and Double-Decoupling Method

Okamoto, Y., Kokubo, H., & Tanaka, T. (2014) · Journal of Chemical Theory and Computation · doi:10.1021/ct500539u · Cited by 11

Sequence specificity in DNA–drug intercalation: MD simulation and density functional theory approaches

Maganti, L., & Bhattacharyya, D. (2019) · Journal of Computer-Aided Molecular Design · doi:10.1007/s10822-019-00268-y · Cited by 11

Exploration of HIV-1 fusion peptide–antibody VRC34.01 binding reveals fundamental neutralization sites

Feng, M., Bell, D. R., Kang, H., Shao, Q., & Zhou, R. (2019) · Physical Chemistry Chemical Physics · doi:10.1039/c9cp02909e · Cited by 10

Accelerating and Automating the Free Energy Perturbation Absolute Binding Free Energy Calculation with the RED-E Function

Liu, R., Li, W., Yao, Y., Wu, Y., Luo, H., & Li, Z. (2023) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.3c01670 · Cited by 10

Separated topologies--a method for relative binding free energy calculations using orientational restraints.

Rocklin, G., Mobley, D., & Dill, K. (2013) · Journal of Chemical Physics · doi:10.1063/1.4792251 · Cited by 43

Accurate Estimation of Protein-ligand Binding Free Energies Based on Geometric Restraints

Fu, H., Chen, H., Zhang, H., Shao, X., & Cai, W. (2021) · 化学学报 · doi:10.6023/a20100489 · Cited by 1

Comparison of Receptor–Ligand Restraint Schemes for Alchemical Absolute Binding Free Energy Calculations

Clark, F., Robb, G. R., Cole, D. J., & Michel, J. (2023) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.3c00139 · Cited by 31

Binding Free Energy Calculation of Small Molecules to Rna with Multiple Binding Poses

Tanida, Y., & Matsuura, A. (2015) · Journal of Computer Chemistry Japan · doi:10.2477/jccj.2015-0029

Extending the scope of alchemical perturbation methods for ligand binding free energy calculations

Fagerberg, E. (2016) · Lund University Publications Student Papers (Lund University)