Using AMBER18 for Relative Free Energy Calculations

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Virtual screening and biological activity evaluation of novel efflux pump inhibitors targeting AdeB

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Discovery of highly potent phosphodiesterase-1 inhibitors by a combined-structure free energy perturbation approach

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AI-Enabled Ultra-large Virtual Screening Identifies Potential Inhibitors of Choline Acetyltransferase for Theranostic Purposes

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Mefloquine reduces the bacterial membrane fluidity of Acinetobacter baumannii and distorts the bacterial membrane when combined with polymyxin B

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A Role of Newly Found Auxiliary Site in Phospholipase A1 from Thai Banded Tiger Wasp (Vespa affinis) in Its Enzymatic Enhancement: In Silico Homology Modeling and Molecular Dynamics Insights

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Relative Binding Free Energy between Chemically Distant Compounds Using a Bidirectional Nonequilibrium Approach

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Hit-to-Lead Optimization of Heterocyclic Carbonyloxycarboximidamides as Selective Antagonists at Human Adenosine A3 Receptor

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Identification of Selective BRD9 Inhibitor via Integrated Computational Approach

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Convergence-Adaptive Roundtrip Method Enables Rapid and Accurate FEP Calculations

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ModBind, a Rapid Simulation-Based Predictor of Ligand Binding and Off-Rates

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Toward Quantum Chemical Accuracy in Absolute Protein–Ligand Binding Free Energy Calculation via Quantum Fragment Method

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Identification of naturally occurring drug-resistant mutations of SARS-CoV-2 papain-like protease

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Relative Binding Free-Energy Calculations at Lipid-Exposed Sites: Deciphering Hot Spots

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Development of an engineered ketoreductase with improved activity, stereoselectivity and relieved substrate inhibition for enantioselective synthesis of a key (R)-α-lipoic acid precursor

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Rational Design of Benzobisheterocycle Metallo-β-Lactamase Inhibitors: A Tricyclic Scaffold Enhances Potency against Target Enzymes

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Water Bridges Play a Key Role in Affinity and Selectivity for Malarial Protease Falcipain-2

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Machine Learning Methods as a Cost-Effective Alternative to Physics-Based Binding Free Energy Calculations

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Engineered Cyclohexylamine Oxidase with Improved Activity and Stereoselectivity for Asymmetric Synthesis of a Bulky Dextromethorphan Precursor and Its Analogues

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In Silico Positional Analogue Scanning with Amber GPU-TI

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A chemoenzymatic strategy for the efficient synthesis of amphenicol antibiotic chloramphenicol mediated by an engineered l -threonine transaldolase with high activity and stereoselectivity

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Molecular Dynamics as a Tool for Virtual Ligand Screening

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An artificial biocatalytic cascade for efficient synthesis of norepinephrine by combination of engineered L-threonine transaldolase with multi-enzyme expression fine-tuning

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The covalent docking software landscape: features and applications in drug design

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2-Arylmelatonin analogues: Probing the 2-phenyl binding pocket of melatonin MT1 and MT2 receptors

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Role of Dynamics and Mutations in Interactions of a Zinc Finger Antiviral Protein with CG-rich Viral RNA

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Study of SQ109 analogs binding to mycobacterium MmpL3 transporter using MD simulations and alchemical relative binding free energy calculations

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Binding Kinetics Toolkit for Analyzing Transient Molecular Conformations and Computing Free Energy Landscapes

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RNF43 Inactivation Enhances the B‐RAF/MEK Signaling and Creates a Combinatory Therapeutic Target in Cancer Cells

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An Efficient Approach to the Accurate Prediction of Mutational Effects in Antigen Binding to the MHC1

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Caught between a ROCK and a hard place: current challenges in structure-based drug design

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Enhancing SILCS-MC via GPU Acceleration and Ligand Conformational Optimization with Genetic and Parallel Tempering Algorithms

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High-level expression and improved pepsin activity by enhancing the conserved domain stability based on a scissor-like model

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Binding of Cholesterol to the N-Terminal Domain of the NPC1L1 Transporter: Analysis of the Epimerization-Related Binding Selectivity and Loop Mutations

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UPLC-ESI–MS/MS phytochemical profile, in vitro, in vivo, and in silico anti-Alzheimer’s activity assessment of Pithecellobium dulce (Roxb.) Benth. leaves

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Accurate calculation of affinity changes to the close state of influenza A M2 transmembrane domain in response to subtle structural changes of adamantyl amines using free energy perturbation methods in different lipid bilayers

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Interface-driven structural evolution on diltiazem as novel uPAR inhibitors: from in silico design to in vitro evaluation

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Accurate Physics-Based Prediction of Binding Affinities of RNA- and DNA-Targeting Ligands

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Rutin from Begonia roxburghii modulates iNOS and Sep A activity in treatment of Shigella flexneri induced diarrhoea in rats: An in vitro, in vivo and computational analysis

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Alchemical Calculation of Relative Free Energies for Charge-Changing Mutations at Protein–Protein Interfaces Considering Fixed and Variable Protonation States

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NE‐RDFE : A protocol and toolkit for computing relative dissociation free energies with GROMACS between dissimilar molecules using bidirectional nonequilibrium dual topology schemes

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MELD-Bracket Ranks Binding Affinities of Diverse Sets of Ligands

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Ligand Binding Affinity Prediction for Membrane Proteins with Alchemical Free Energy Calculation Methods

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Synergistic insights into positive allosteric modulator and agonist using Gaussian accelerated and tau random acceleration simulations in the metabotropic glutamate receptor 2

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Prediction of potential drug-resistant ALK mutations against fourth-generation inhibitors NVL-655 and TPX-0131

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Fragment Molecular Orbital Based Affinity Prediction toward Pyruvate Dehydrogenase Kinases: Insights into the Charge Transfer in Hydrogen Bond Networks

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Understanding base and backbone contributions of phosphorothioate DNA for molecular recognition with SBD proteins

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Rational design of short‐chain dehydrogenase/reductase for enantio‐complementary synthesis of chiral 1,2‐diols by successive hydroxymethylation and reduction of aldehydes

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Introduction to Comprehensive Glycoscience: The Good, the Better and What's to Come

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Disruption of Water Networks is the Cause of Human/Mouse Species Selectivity in Urokinase Plasminogen Activator (uPA) Inhibitors Derived from Hexamethylene Amiloride (HMA)

Salamouni, N. S. E., Buckley, B. J., Jiang, L., Huang, M., Ranson, M., Kelso, M. J., & Yu, H. B. (2021) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.1c01423 · Cited by 5

Prospective Application of Free Energy Methods in Drug Discovery Programs

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Integrated Strategies for Designing Novel Thiazolidine-2, 4-Dione-Oxazole Derivatives as PPAR-γ Agonists: 3D-QSAR, Virtual Screening and Molecular Dynamics Simulations

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Cheminformatics-driven discovery of natural isoquinoline alkaloid inhibitors of Beta-secretase I for Alzheimer’s management

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Could statistical potential models achieve comparable or better performance than deep learning models?

Wang, Z., Wang, S., Guo, J., Mu, Y., Liu, X., Zheng, L., & Li, W. (2026) · Briefings in Bioinformatics · doi:10.1093/bib/bbag088 · Cited by 4

System truncation accelerates binding affinity calculations with the fragment molecular orbital method: A benchmark study

Nakamura, S., Akaki, T., Nishiwaki, K., Nakatani, M., Kawase, Y., Takahashi, Y., & Nakanishi, I. (2022) · Journal of Computational Chemistry · doi:10.1002/jcc.27044 · Cited by 4

Identification of novel LRRK2 inhibitors by structure-based virtual screening and alchemical free energy calculation

Tan, S., Gong, X., Liu, H., & Yao, X. (2024) · Physical Chemistry Chemical Physics · doi:10.1039/d4cp01762e · Cited by 4

Designing of a multiepitope-based vaccine against echinococcosis utilizing the potent Ag5 antigen: Immunoinformatics and simulation approaches

Parvin, R., Masum, M. H. U., Heema, H. P., Akter, A., Hossain, M. A., & Siddiki, A. Z. (2025) · PLoS ONE · doi:10.1371/journal.pone.0310510 · Cited by 4

Automated On-the-Fly Optimization of Resource Allocation for Efficient Free Energy Simulations

Koby, S. B., Gutkin, E. M., Patel, S., & Kurnikova, M. G. (2025) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.4c02107 · Cited by 5

Comprehensive, Open-Source, and Automated Workflow for Multisite λ-Dynamics in Lead Optimization

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Assessment of the Topology and Oligomerisation States of Coiled Coils Using Metadynamics with Conformational Restraints

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N‑[(Thiophen-3-yl)methyl]benzamides as Fusion Inhibitors of Influenza Virus Targeting H1 and H5 Hemagglutinins

Rimaux, S., Valdivia, A., Martín-López, J., Francesconi, V., Escriche, C., Mestdagh, C., Berwaer, R. V., Schurmans, L., Verleye, K., Noppen, S., et al. (2025) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.5c01357 · Cited by 3

Practical guidelines for optimising free energy calculations using thermodynamic integration

Knirsch, A., Falcone, B. N., & Hirst, J. D. (2025) · Chemical Physics Letters · doi:10.1016/j.cplett.2025.142395 · Cited by 3

Multi-strategy engineering of transaminase enables a one-pot synergistic biocatalytic cascade to a key florfenicol chiral intermediate

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Engineered Monoamine Oxidase-Catalyzed Deracemization of Sterically Hindered Acylaminomethyl-tetrahydroisoquinoline: Asymmetric Synthesis of (R)-(−)-Praziquantel and Its Analogues

Liu, J., Wu, X., Li, Z., Huang, Z., & Chen, F. (2023) · ACS Sustainable Chemistry & Engineering · doi:10.1021/acssuschemeng.3c00985 · Cited by 3

Screening of the antileishmanial and antiplasmodial potential of synthetic 2-arylquinoline analogs

Espinosa-Sáez, R., Robledo, S. M., Pineda, T., Murillo, J. D., Zúñiga, C., Yáñez, O., Cantero-López, P., Sáez, A. A., & Guzmán, C. (2023) · Scientific Reports · doi:10.1038/s41598-023-43805-4 · Cited by 3

Effect of Protein-Polarized Ligand Charges on Relative Protein Ligand Binding Affinities

Adam, S., Kass, I., Zussman, D. K., Masarati, G., Shemesh, D., & Sharir‐Ivry, A. (2024) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.3c01337 · Cited by 3

Modeling Ligand Binding Site Water Networks with Site Identification by Ligand Competitive Saturation: Impact on Ligand Binding Orientations and Relative Binding Affinities

Kumar, A., Goel, H., Yu, W., Zhao, M., & MacKerell, A. D. (2024) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.4c01165 · Cited by 4

Thermodynamic integration combined with molecular dynamic simulations to explore the cross‐resistance mechanism of isoniazid and ethionamide

Zhang, Q., Yang, Y., Gong, X., Zhao, N., Zhang, Y., & Liu, H. (2022) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.26295 · Cited by 3

HTP SurflexDock: a web tool for Structure-Based Virtual Screening analysis based on the Ensemble Docking protocol

Filho, J. L. D. A., & Fernández, J. H. (2022) · doi:10.5753/bresci.2022.223295 · Cited by 3

Preclinical Studies and Drug Combination of Low-Cost Molecules for Chagas Disease

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TIES 2.0: A Dual-Topology Open Source Relative Binding Free Energy Builder with Web Portal

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Further exploration of the quantitative distance-energy and contact number-energy relationships for predicting the binding affinity of protein-ligand complexes

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Comparative Analysis of Quantum-Mechanical and Standard Single-Structure Protein–Ligand Scoring Functions with MD-Based Free Energy Calculations

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Advanced Computational Modeling Accelerating Small‐Molecule Drug Discovery

Abel, R. (2022) · Wiley eBooks · doi:10.1002/9781119627784.ch2 · Cited by 3

An Automated On-The-Fly Optimization of Resource Allocation for High-Throughput Protein-Ligand Binding Free Energy SimulationsPreprint

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Binding Selectivity of Inhibitors to BRD2 Uncovered by Molecular Docking and Molecular Dynamics Simulations

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