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Accurate calculation of the absolute free energy of binding for drug molecules

https://doi.org/10.1039/c5sc02678d
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Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Computational methods to examine conformational changes and ligand-binding properties: Examples in neurobiology
inferred← citeshttps://doi.org/10.1016/j.neuropharm.2025.110351openalex-snapshot
Synergistic insights into positive allosteric modulator and agonist using Gaussian accelerated and tau random acceleration simulations in the metabotropic glutamate receptor 2
inferred← citeshttps://doi.org/10.1016/j.sbi.2018.09.002openalex-snapshot
Modeling the value of predictive affinity scoring in preclinical drug discovery
inferred← citeshttps://doi.org/10.1016/j.sbi.2021.08.003openalex-snapshot
Recent developments in multiscale free energy simulations
inferred← citeshttps://doi.org/10.1016/j.virusres.2020.197989openalex-snapshot
Natural product-derived phytochemicals as potential agents against coronaviruses: A review
inferred← citeshttps://doi.org/10.1021/acs.chemrev.0c00534openalex-snapshot
Thermodynamics and Kinetics of Drug-Target Binding by Molecular Simulation
inferred← citeshttps://doi.org/10.1021/acs.jcim.0c00116openalex-snapshot
Rigorous Free Energy Simulations in Virtual Screening
inferred← citeshttps://doi.org/10.1021/acs.jcim.0c00338openalex-snapshot
Prediction of Protein–Ligand Binding Pose and Affinity Using the gREST+FEP Method
inferred← citeshttps://doi.org/10.1021/acs.jcim.0c00558openalex-snapshot
An ABSINTH-Based Protocol for Predicting Binding Affinities between Proteins and Small Molecules
inferred← citeshttps://doi.org/10.1021/acs.jcim.0c00607openalex-snapshot
Diameter Is a Key 3D Characteristic for Assessments of Efficient Inhibitors of Protein–Protein Interactions
inferred← citeshttps://doi.org/10.1021/acs.jcim.0c00610openalex-snapshot
Identification of Optimal Ligand Growth Vectors Using an Alchemical Free-Energy Method
inferred← citeshttps://doi.org/10.1021/acs.jcim.0c00853openalex-snapshot
Efficient Refinement and Free Energy Scoring of Predicted Protein–Protein Complexes Using Replica Exchange with Repulsive Scaling
inferred← citeshttps://doi.org/10.1021/acs.jcim.0c00900openalex-snapshot
Large-Scale Assessment of Binding Free Energy Calculations in Active Drug Discovery Projects
inferred← citeshttps://doi.org/10.1021/acs.jcim.0c01146openalex-snapshot
Ligand Entropy Is Hard but Should Not Be Ignored
inferred← citeshttps://doi.org/10.1021/acs.jcim.1c00515openalex-snapshot
Predicting the Relative Binding Affinity for Reversible Covalent Inhibitors by Free Energy Perturbation Calculations
inferred← citeshttps://doi.org/10.1021/acs.jcim.1c00897openalex-snapshot
Modeling the Binding and Conformational Energetics of a Targeted Covalent Inhibitor to Bruton’s Tyrosine Kinase
inferred← citeshttps://doi.org/10.1021/acs.jcim.1c01189openalex-snapshot
Tetracycline Derivatives Inhibit Plasmodial Cysteine Protease Falcipain-2 through Binding to a Distal Allosteric Site
inferred← citeshttps://doi.org/10.1021/acs.jcim.1c01229openalex-snapshot
Alchemical Free Energy Methods Applied to Complexes of the First Bromodomain of BRD4
inferred← citeshttps://doi.org/10.1021/acs.jcim.1c01399openalex-snapshot
Deciphering the Mechanism of Binding Selectivity of Chlorofluoroacetamide-Based Covalent Inhibitors toward L858R/T790M Resistance Mutation
inferred← citeshttps://doi.org/10.1021/acs.jcim.2c00417openalex-snapshot
Mechanistic Studies on the Stereoselectivity of FFAR1 Modulators
inferred← citeshttps://doi.org/10.1021/acs.jcim.3c00013openalex-snapshot
Enhancing Hit Discovery in Virtual Screening through Absolute Protein–Ligand Binding Free-Energy Calculations
inferred← citeshttps://doi.org/10.1021/acs.jcim.3c00122openalex-snapshot
Leveraging Advanced In Silico Techniques in Early Drug Discovery: A Study of Potent Small-Molecule YAP-TEAD PPI Disruptors
inferred← citeshttps://doi.org/10.1021/acs.jcim.3c00253openalex-snapshot
PLANET: A Multi-objective Graph Neural Network Model for Protein–Ligand Binding Affinity Prediction
inferred← citeshttps://doi.org/10.1021/acs.jcim.3c00681openalex-snapshot
FEP Protocol Builder: Optimization of Free Energy Perturbation Protocols Using Active Learning
inferred← citeshttps://doi.org/10.1021/acs.jcim.3c00874openalex-snapshot
Computation of Absolute Binding Free Energies for Noncovalent Inhibitors with SARS-CoV-2 Main Protease
inferred← citeshttps://doi.org/10.1021/acs.jcim.3c01041openalex-snapshot
Computed Protein–Protein Enthalpy Signatures as a Tool for Identifying Conformation Sampling Problems
inferred← citeshttps://doi.org/10.1021/acs.jcim.3c01379openalex-snapshot
Structure-Based Optimization of Carbendazim-Derived Tubulin Polymerization Inhibitors through Alchemical Free Energy Calculations
inferred← citeshttps://doi.org/10.1021/acs.jcim.3c01469openalex-snapshot
Accelerating Alchemical Free Energy Prediction Using a Multistate Method: Application to Multiple Kinases
inferred← citeshttps://doi.org/10.1021/acs.jcim.3c01670openalex-snapshot
Accelerating and Automating the Free Energy Perturbation Absolute Binding Free Energy Calculation with the RED-E Function
inferred← citeshttps://doi.org/10.1021/acs.jcim.4c00343openalex-snapshot
Automated Absolute Binding Free Energy Calculation Workflow for Drug Discovery
inferred← citeshttps://doi.org/10.1021/acs.jcim.4c00764openalex-snapshot
Ligand Binding Affinity Prediction for Membrane Proteins with Alchemical Free Energy Calculation Methods
inferred← citeshttps://doi.org/10.1021/acs.jcim.4c01088openalex-snapshot
Analysis of Glycan Recognition by Concanavalin A Using Absolute Binding Free Energy Calculations
inferred← citeshttps://doi.org/10.1021/acs.jcim.4c01668openalex-snapshot
Adaptive Lambda Scheduling: A Method for Computational Efficiency in Free Energy Perturbation Simulations
inferred← citeshttps://doi.org/10.1021/acs.jcim.4c01710openalex-snapshot
Konnektor: A Framework for Using Graph Theory to Plan Networks for Free Energy Calculations
inferred← citeshttps://doi.org/10.1021/acs.jcim.4c01986openalex-snapshot
FEP-SPell-ABFE: An Open-Source Automated Alchemical Absolute Binding Free-Energy Calculation Workflow for Drug Discovery
inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00644openalex-snapshot
The Fragment Molecular Orbital Method Reveals New Insight into the Chemical Nature of GPCR–Ligand Interactions
inferred← citeshttps://doi.org/10.1021/acs.jcim.5c00947openalex-snapshot
Quantification of the Impact of Structure Quality on Predicted Binding Free Energy Accuracy
inferred← citeshttps://doi.org/10.1021/acs.jcim.5c02204openalex-snapshot
A Relative Binding Free Energy Framework for Structurally Dissimilar Molecules
inferred← citeshttps://doi.org/10.1021/acs.jcim.5c03127openalex-snapshot
A Neural Time-Series Learning Method for Accelerating Free-Energy Perturbation and Rare-Event Molecular Dynamics Simulations
inferred← citeshttps://doi.org/10.1021/acs.jcim.6b00290openalex-snapshot
Computational Modeling of β-Secretase 1 (BACE-1) Inhibitors Using Ligand Based Approaches
inferred← citeshttps://doi.org/10.1021/acs.jcim.6b00362openalex-snapshot
Relative Binding Free Energy Calculations Applied to Protein Homology Models
inferred← citeshttps://doi.org/10.1021/acs.jcim.7b00347openalex-snapshot
Statistical Analysis on the Performance of Molecular Mechanics Poisson–Boltzmann Surface Area versus Absolute Binding Free Energy Calculations: Bromodomains as a Case Study
inferred← citeshttps://doi.org/10.1021/acs.jcim.7b00485openalex-snapshot
Comparative Assessment of Computational Methods for Free Energy Calculations of Ionic Hydration
inferred← citeshttps://doi.org/10.1021/acs.jcim.8b00779openalex-snapshot
Ligity: A Non-Superpositional, Knowledge-Based Approach to Virtual Screening
inferred← citeshttps://doi.org/10.1021/acs.jcim.9b00228openalex-snapshot
Computational Fluorine Scanning Using Free-Energy Perturbation
inferred← citeshttps://doi.org/10.1021/acs.jcim.9b00528openalex-snapshot
Optimal Measurement Network of Pairwise Differences
inferred← citeshttps://doi.org/10.1021/acs.jctc.0c00075openalex-snapshot
Combining Machine Learning and Enhanced Sampling Techniques for Efficient and Accurate Calculation of Absolute Binding Free Energies
inferred← citeshttps://doi.org/10.1021/acs.jctc.0c00163openalex-snapshot
Repulsive Soft-Core Potentials for Efficient Alchemical Free Energy Calculations
inferred← citeshttps://doi.org/10.1021/acs.jctc.0c00752openalex-snapshot
Reversibly Sampling Conformations and Binding Modes Using Molecular Darting
inferred← citeshttps://doi.org/10.1021/acs.jctc.0c01305openalex-snapshot
Estimating the Roles of Protonation and Electronic Polarization in Absolute Binding Affinity Simulations
inferred← citeshttps://doi.org/10.1021/acs.jctc.1c00513openalex-snapshot
Expanded Ensemble Methods Can be Used to Accurately Predict Protein-Ligand Relative Binding Free Energies
inferred← citeshttps://doi.org/10.1021/acs.jctc.1c00703openalex-snapshot
Precise Binding Free Energy Calculations for Multiple Molecules Using an Optimal Measurement Network of Pairwise Differences
inferred← citeshttps://doi.org/10.1021/acs.jctc.1c01208openalex-snapshot
Comparing the Performance of Different AMBER Protein Forcefields, Partial Charge Assignments, and Water Models for Absolute Binding Free Energy Calculations
inferred← citeshttps://doi.org/10.1021/acs.jctc.1c01251openalex-snapshot
Correction Schemes for Absolute Binding Free Energies Involving Lipid Bilayers
inferred← citeshttps://doi.org/10.1021/acs.jctc.1c01288openalex-snapshot
Large Scale Study of Ligand–Protein Relative Binding Free Energy Calculations: Actionable Predictions from Statistically Robust Protocols
inferred← citeshttps://doi.org/10.1021/acs.jctc.2c00114openalex-snapshot
Alchemical Free Energy Estimators and Molecular Dynamics Engines: Accuracy, Precision, and Reproducibility
inferred← citeshttps://doi.org/10.1021/acs.jctc.2c00295openalex-snapshot
Relative Binding Free Energy between Chemically Distant Compounds Using a Bidirectional Nonequilibrium Approach
inferred← citeshttps://doi.org/10.1021/acs.jctc.3c00282openalex-snapshot
Broadening the Scope of Binding Free Energy Calculations Using a Separated Topologies Approach
inferred← citeshttps://doi.org/10.1021/acs.jctc.3c00365openalex-snapshot
Alchemical Free Energy Calculations on Membrane-Associated Proteins
inferred← citeshttps://doi.org/10.1021/acs.jctc.3c01050openalex-snapshot
Tuning Potential Functions to Host–Guest Binding Data
inferred← citeshttps://doi.org/10.1021/acs.jctc.3c01206openalex-snapshot
Kartograf: A Geometrically Accurate Atom Mapper for Hybrid-Topology Relative Free Energy Calculations
inferred← citeshttps://doi.org/10.1021/acs.jctc.4c00057openalex-snapshot
Calculations of Absolute Free Energies, Enthalpies, and Entropies for Drug Binding
inferred← citeshttps://doi.org/10.1021/acs.jctc.4c00205openalex-snapshot
BAT2: an Open-Source Tool for Flexible, Automated, and Low Cost Absolute Binding Free Energy Calculations
inferred← citeshttps://doi.org/10.1021/acs.jctc.4c00939openalex-snapshot
Convergence-Adaptive Roundtrip Method Enables Rapid and Accurate FEP Calculations
inferred← citeshttps://doi.org/10.1021/acs.jctc.4c01112openalex-snapshot
Host–Guest Binding Free Energies à la Carte: An Automated OneOPES Protocol
inferred← citeshttps://doi.org/10.1021/acs.jctc.4c01389openalex-snapshot
Equilibrium and Nonequilibrium Ensemble Methods for Accurate, Precise and Reproducible Absolute Binding Free Energy Calculations
inferred← citeshttps://doi.org/10.1021/acs.jctc.4c01661openalex-snapshot
Divide-and-Conquer ABFE: Improving Free Energy Calculations by Enhancing Water Sampling
inferred← citeshttps://doi.org/10.1021/acs.jctc.4c01695openalex-snapshot
Assessment of the Topology and Oligomerisation States of Coiled Coils Using Metadynamics with Conformational Restraints
inferred← citeshttps://doi.org/10.1021/acs.jctc.5c00121openalex-snapshot
Applying Absolute Free Energy Perturbation Molecular Dynamics to Diffusively Binding Ligands
inferred← citeshttps://doi.org/10.1021/acs.jctc.5c00861openalex-snapshot
Optimizing Absolute Binding Free Energy Calculations for Production Usage
inferred← citeshttps://doi.org/10.1021/acs.jctc.5c01640openalex-snapshot
ANUBI: A Platform for Affinity Optimization of Proteins and Peptides in Drug Design
inferred← citeshttps://doi.org/10.1021/acs.jctc.5c02026openalex-snapshot
BindFlow: A Free, User-Friendly Pipeline for Absolute Binding Free Energy Calculations Using Free Energy Perturbation or MM(PB/GB)SA
inferred← citeshttps://doi.org/10.1021/acs.jctc.6b00794openalex-snapshot
Rapid and Reliable Binding Affinity Prediction of Bromodomain Inhibitors: A Computational Study
inferred← citeshttps://doi.org/10.1021/acs.jctc.6b00979openalex-snapshot
Rapid, Accurate, Precise, and Reliable Relative Free Energy Prediction Using Ensemble Based Thermodynamic Integration
inferred← citeshttps://doi.org/10.1021/acs.jctc.6b01217openalex-snapshot
Comparison of QM/MM Methods To Obtain Ligand-Binding Free Energies
inferred← citeshttps://doi.org/10.1021/acs.jctc.6c00930openalex-snapshot
Charged Systems in Absolute Binding Free Energy Calculations: An Analytical Electrostatic Approach
inferred← citeshttps://doi.org/10.1021/acs.jctc.7b00275openalex-snapshot
Attach-Pull-Release Calculations of Ligand Binding and Conformational Changes on the First BRD4 Bromodomain
inferred← citeshttps://doi.org/10.1021/acs.jctc.7b00791openalex-snapshot
New Coarse Variables for the Accurate Determination of Standard Binding Free Energies
inferred← citeshttps://doi.org/10.1021/acs.jctc.7b01143openalex-snapshot
Uncertainty Quantification in Alchemical Free Energy Methods
inferred← citeshttps://doi.org/10.1021/acs.jctc.8b00418openalex-snapshot
Simple Entropy Terms for End-Point Binding Free Energy Calculations
inferred← citeshttps://doi.org/10.1021/acs.jctc.8b00821openalex-snapshot
Toward Learned Chemical Perception of Force Field Typing Rules
inferred← citeshttps://doi.org/10.1021/acs.jctc.9b00213openalex-snapshot
Robust Free Energy Perturbation Protocols for Creating Molecules in Solution
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.2c00796openalex-snapshot
Meta-Analysis Reveals That Absolute Binding Free-Energy Calculations Approach Chemical Accuracy
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.4c03087openalex-snapshot
Computational Hit Finding: An Industry Perspective
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.7b00681openalex-snapshot
Free Energy Methods in Drug Design: Prospects of “Alchemical Perturbation” in Medicinal Chemistry
inferred← citeshttps://doi.org/10.1021/acs.jpcb.0c11383openalex-snapshot
Evaluating the Performance of Water Models with Host–Guest Force Fields in Binding Enthalpy Calculations for Cucurbit[7]uril–Guest Systems
inferred← citeshttps://doi.org/10.1021/acs.jpcb.1c10278openalex-snapshot
Prediction of COMT Inhibitors Using Machine Learning and Molecular Dynamics Methods
inferred← citeshttps://doi.org/10.1021/acs.jpcb.2c04641openalex-snapshot
Electrostatic Contributions to the Binding Free Energy of Nicotine to the Acetylcholine Binding Protein
inferred← citeshttps://doi.org/10.1021/acs.jpcb.3c06516openalex-snapshot
Addressing Suboptimal Poses in Nonequilibrium Alchemical Calculations
inferred← citeshttps://doi.org/10.1021/acs.jpcb.4c00310openalex-snapshot
Molecular Insights into the Impact of Mutations on the Binding Affinity of Targeted Covalent Inhibitors of BTK
inferred← citeshttps://doi.org/10.1021/acs.jpcb.4c07569openalex-snapshot
Calculations of the Absolute Free Energy, Enthalpy, and Entropy of Drug Binding Using Different Potential Models
inferred← citeshttps://doi.org/10.1021/acs.jpcb.5c06714openalex-snapshot
Toward Reconciling the Standard Binding Free Energy of Lenacapavir to HIV-1 Capsid with Experiment: Thermodynamic Effects of Solvent Buffer and Ligand Reorganization
inferred← citeshttps://doi.org/10.1021/acs.jpcb.6c00354openalex-snapshot
D-MBIS Nonbonded Force Field Parameters Improve Specificity and Selectivity Prediction in Bromodomains
inferred← citeshttps://doi.org/10.1021/acs.jpcb.6c00969openalex-snapshot
Free-Energy Calculations of Biomolecular Processes: Methods Development, Benchmarking, and Applications
inferred← citeshttps://doi.org/10.1021/acs.jpclett.2c03126openalex-snapshot
Molecular Thermodynamic Origin of Substrate Promiscuity in the Enzyme Laccase: Toward a Broad-Spectrum Degrader of Dye Effluents
inferred← citeshttps://doi.org/10.1021/acs.jpclett.4c02656openalex-snapshot
RED-E-Function-Based Equilibrium Parameter Finder: Finding the Best Restraint Parameters in Absolute Binding Free Energy Calculations
inferred← citeshttps://doi.org/10.1021/acs.jpclett.5c00683openalex-snapshot
Lambda-ABF-OPES: Faster Convergence with High Accuracy in Alchemical Free Energy Calculations
inferred← citeshttps://doi.org/10.1021/acsbiomedchemau.3c00046openalex-snapshot
Shape-Based Virtual Screening of a Billion-Compound Library Identifies Mycobacterial Lipoamide Dehydrogenase Inhibitors
inferred← citeshttps://doi.org/10.1021/acschemneuro.7b00215openalex-snapshot
Effect of Alzheimer Familial Chromosomal Mutations on the Amyloid Fibril Interaction with Different PET Tracers: Insight from Molecular Modeling Studies
inferred← citeshttps://doi.org/10.1021/acschemneuro.7b00490openalex-snapshot
What Contributes to Serotonin–Norepinephrine Reuptake Inhibitors’ Dual-Targeting Mechanism? The Key Role of Transmembrane Domain 6 in Human Serotonin and Norepinephrine Transporters Revealed by Molecular Dynamics Simulation
inferred← citeshttps://doi.org/10.1021/acschemneuro.9b00348openalex-snapshot
Molecular Mechanism of Binding Selectivity of Inhibitors toward BACE1 and BACE2 Revealed by Multiple Short Molecular Dynamics Simulations and Free-Energy Predictions
inferred← citeshttps://doi.org/10.1021/acsomega.2c00729openalex-snapshot
Unveiling the Possible Oryzalin-Binding Site in the α‑Tubulin of Toxoplasma gondii
inferred← citeshttps://doi.org/10.1021/acsomega.3c03935openalex-snapshot
Selectivity Mechanism of Pyrrolopyridone Analogues Targeting Bromodomain 2 of Bromodomain-Containing Protein 4 from Molecular Dynamics Simulations
inferred← citeshttps://doi.org/10.1021/acsomega.4c08049openalex-snapshot
Molecular Glue-Design-Evaluator (MOLDE): An Advanced Method for In-Silico Molecular Glue Design
inferred← citeshttps://doi.org/10.1021/acsomega.5c00151openalex-snapshot
Acceleration of the GROMACS Free-Energy Perturbation Calculations on GPUs
inferred← citeshttps://doi.org/10.1021/acsomega.7b00553openalex-snapshot
Identification of a Novel Class of BRD4 Inhibitors by Computational Screening and Binding Simulations
inferred← citeshttps://doi.org/10.1021/acsomega.8b02354openalex-snapshot
Effect of Substituents in Different Positions of Aminothiazole Hinge-Binding Scaffolds on Inhibitor–CDK2 Association Probed by Interaction Entropy Method
inferred← citeshttps://doi.org/10.1021/bk-2021-1397.ch002openalex-snapshot
Use of Free Energy Methods in the Drug Discovery Industry
inferred← citeshttps://doi.org/10.1021/jacs.6b11467openalex-snapshot
Predictions of Ligand Selectivity from Absolute Binding Free Energy Calculations
inferred← citeshttps://doi.org/10.1038/s41467-022-32192-5openalex-snapshot
Non-fluorinated non-solvating cosolvent enabling superior performance of lithium metal negative electrode battery
inferred← citeshttps://doi.org/10.1038/s41467-026-68941-zopenalex-snapshot
Developments and challenges in hit progression within fragment-based drug discovery
inferred← citeshttps://doi.org/10.1038/s41596-020-0342-4openalex-snapshot
Ligand binding free-energy calculations with funnel metadynamics
inferred← citeshttps://doi.org/10.1038/s41598-019-41758-1openalex-snapshot
Application of ESMACS binding free energy protocols to diverse datasets: Bromodomain-containing protein 4
inferred← citeshttps://doi.org/10.1038/s41598-020-80769-1openalex-snapshot
Automation of absolute protein-ligand binding free energy calculations for docking refinement and compound evaluation
inferred← citeshttps://doi.org/10.1038/s41598-022-17480-wopenalex-snapshot
Absolute binding free energy calculations improve enrichment of actives in virtual compound screening
inferred← citeshttps://doi.org/10.1038/s41598-023-45269-yopenalex-snapshot
Binding affinity predictions with hybrid quantum-classical convolutional neural networks
inferred← citeshttps://doi.org/10.1038/s42003-018-0075-xopenalex-snapshot
Predicting resistance of clinical Abl mutations to targeted kinase inhibitors using alchemical free-energy calculations
inferred← citeshttps://doi.org/10.1038/s42003-022-03416-7openalex-snapshot
Differences in ligand-induced protein dynamics extracted from an unsupervised deep learning approach correlate with protein–ligand binding affinities
inferred← citeshttps://doi.org/10.1038/s42003-024-06906-yopenalex-snapshot
Cyclopamine modulates smoothened receptor activity in a binding position dependent manner
inferred← citeshttps://doi.org/10.1038/s42004-021-00498-yopenalex-snapshot
Accurate absolute free energies for ligand–protein binding based on non-equilibrium approaches
inferred← citeshttps://doi.org/10.1038/s42004-022-00721-4openalex-snapshot
Evaluating the use of absolute binding free energy in the fragment optimisation process
inferred← citeshttps://doi.org/10.1038/s42004-023-00859-9openalex-snapshot
Automated relative binding free energy calculations from SMILES to ΔΔG
inferred← citeshttps://doi.org/10.1038/s42004-024-01328-7openalex-snapshot
Accurate protein-ligand binding free energy estimation using QM/MM on multi-conformers predicted from classical mining minima
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