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Binding Free Energy Calculations for Lead Optimization: Assessment of Their Accuracy in an Industrial Drug Design Context
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inferredcites →https://doi.org/10.1002/(sici)1096-987x(20000130)21:2<132::aid-jcc5>3.0.co;2-popenalex-snapshot
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inferredcites →https://doi.org/10.1002/(sici)1097-0134(19990215)34:3<395::aid-prot11>3.0.co;2-4openalex-snapshot
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inferredcites →https://doi.org/10.1002/1097-0282(2000)56:4<275::aid-bip10024>3.0.co;2-eopenalex-snapshot
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inferredcites →https://doi.org/10.1002/ange.201004575openalex-snapshot
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inferredcites →https://doi.org/10.1016/j.bmc.2007.08.019openalex-snapshot
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inferredcites →https://doi.org/10.1016/j.healthpol.2010.12.002openalex-snapshot
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inferredcites →https://doi.org/10.1016/j.jmb.2009.11.011openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/9783527840748.ch1openalex-snapshot
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Alchemical Free Energy Calculations and Isothermal Titration Calorimetry Measurements of Aminoadamantanes Bound to the Closed State of Influenza A/M2TM
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.6b00373openalex-snapshot
Efficient Approximation of Ligand Rotational and Translational Entropy Changes upon Binding for Use in MM-PBSA Calculations
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.7b00455openalex-snapshot
Discovery of Novel Adenosine Receptor Antagonists through a Combined Structure- and Ligand-Based Approach Followed by Molecular Dynamics Investigation of Ligand Binding Mode
inferred← citeshttps://doi.org/10.1021/acs.jcim.8b00120openalex-snapshot
Defining the Specificity of Carbohydrate–Protein Interactions by Quantifying Functional Group Contributions
inferred← citeshttps://doi.org/10.1021/acs.jcim.8b00462openalex-snapshot
GPU-Accelerated Molecular Dynamics and Free Energy Methods in Amber18: Performance Enhancements and New Features
inferred← citeshttps://doi.org/10.1021/acs.jcim.8b00765openalex-snapshot
Energetic Fingerprinting of Ligand Binding to Paralogous Proteins: The Case of the Apoptotic Pathway
inferred← citeshttps://doi.org/10.1021/acs.jcim.9b00751openalex-snapshot
Insights to the Binding of a Selective Adenosine A 3 Receptor Antagonist Using Molecular Dynamic Simulations, MM-PBSA and MM-GBSA Free Energy Calculations, and Mutagenesis
inferred← citeshttps://doi.org/10.1021/acs.jcim.9b01118openalex-snapshot
Impact of Different Automated Binding Pose Generation Approaches on Relative Binding Free Energy Simulations
inferred← citeshttps://doi.org/10.1021/acs.jctc.0c00249openalex-snapshot
Mechanism of Fully Reversible, pH-Sensitive Inhibition of Human Glutamine Synthetase by Tyrosine Nitration
inferred← citeshttps://doi.org/10.1021/acs.jctc.1c01271openalex-snapshot
Drug Discovery by Automated Adaptation of Chemical Structure and Identity
inferred← citeshttps://doi.org/10.1021/acs.jctc.4c01268openalex-snapshot
Multiple Topology Replica Exchange of Expanded Ensembles for Multidimensional Alchemical Calculations
inferred← citeshttps://doi.org/10.1021/acs.jctc.4c01427openalex-snapshot
Evaluation of Machine Learning/Molecular Mechanics End-State Corrections with Mechanical Embedding to Calculate Relative Protein–Ligand Binding Free Energies
inferred← citeshttps://doi.org/10.1021/acs.jctc.5b00159openalex-snapshot
Evaluation of Selected Classical Force Fields for Alchemical Binding Free Energy Calculations of Protein-Carbohydrate Complexes
inferred← citeshttps://doi.org/10.1021/acs.jctc.6b00532openalex-snapshot
Sensitivity in Binding Free Energies Due to Protein Reorganization
inferred← citeshttps://doi.org/10.1021/acs.jctc.6b01141openalex-snapshot
Acylguanidine Beta Secretase 1 Inhibitors: A Combined Experimental and Free Energy Perturbation Study
inferred← citeshttps://doi.org/10.1021/acs.jctc.7b00014openalex-snapshot
Rigidity Theory-Based Approximation of Vibrational Entropy Changes upon Binding to Biomolecules
inferred← citeshttps://doi.org/10.1021/acs.jctc.7b00102openalex-snapshot
Toward Fast and Accurate Binding Affinity Prediction with pmemdGTI: An Efficient Implementation of GPU-Accelerated Thermodynamic Integration
inferred← citeshttps://doi.org/10.1021/acs.jctc.8b00685openalex-snapshot
Predicting Relative Binding Affinity Using Nonequilibrium QM/MM Simulations
inferred← citeshttps://doi.org/10.1021/acs.jctc.8b00687openalex-snapshot
A Multiscale Simulation Approach to Modeling Drug–Protein Binding Kinetics
inferred← citeshttps://doi.org/10.1021/acs.jctc.8b01280openalex-snapshot
Host–Guest Relative Binding Affinities at Density-Functional Theory Level from Semiempirical Molecular Dynamics Simulations
inferred← citeshttps://doi.org/10.1021/acs.jctc.8b01290openalex-snapshot
Predicting Activity Cliffs with Free-Energy Perturbation
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.5c03756openalex-snapshot
A Systematic Benchmark Study of Free Energy Methods for Quantifying Light-Responsive Binding Affinities of Photoswitchable Antagonists of Beta-Adrenergic Receptors
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.6b01881openalex-snapshot
Prospective Evaluation of Free Energy Calculations for the Prioritization of Cathepsin L Inhibitors
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.9b01164openalex-snapshot
Structural Characterization of Agonist Binding to an A 3 Adenosine Receptor through Biomolecular Simulations and Mutagenesis Experiments
inferred← citeshttps://doi.org/10.1021/acs.jpcb.3c00834openalex-snapshot
Revisiting MMPBSA by Adoption of MC-Based Surface Area/Volume, ANI-ML Potentials, and Two-Valued Interior Dielectric Constant
inferred← citeshttps://doi.org/10.1021/acs.jpcb.3c05986openalex-snapshot
Computational Workflow for Refining AlphaFold Models in Drug Design Using Kinetic and Thermodynamic Binding Calculations: A Case Study for the Unresolved Inactive Human Adenosine A 3 Receptor
inferred← citeshttps://doi.org/10.1021/acs.jpcb.4c02325openalex-snapshot
A Study on the Binding Mechanism and the Impact of Key Residue Mutations between SND1 and MTDH Peptide through Molecular Dynamics Simulations
inferred← citeshttps://doi.org/10.1021/acs.jpcb.5c02125openalex-snapshot
Investigating the Interaction Mechanism of CAT-BT-Br and Key Residue Mutations for Castration-Resistant Prostate Cancer through Molecular Dynamics Simulation
inferred← citeshttps://doi.org/10.1021/acs.jpcb.8b03245openalex-snapshot
A Linear Interaction Energy Model for Cavitand Host–Guest Binding Affinities
inferred← citeshttps://doi.org/10.1021/acs.macromol.0c01896openalex-snapshot
Cumulative Submillisecond All-Atom Simulations of the Temperature-Induced Coil-to-Globule Transition of Poly( N -vinylcaprolactam) in Aqueous Solution
inferred← citeshttps://doi.org/10.1021/acschembio.3c00402openalex-snapshot
Discovery of Nonretinoid Inhibitors of CRBP1: Structural and Dynamic Insights for Ligand-Binding Mechanisms
inferred← citeshttps://doi.org/10.1021/acsmedchemlett.4c00631openalex-snapshot
Thiosulfonate-Based Targeted Covalent Cruzipain Inhibitors with Enhanced Bioactivity Translation for Antichagasic Therapy
inferred← citeshttps://doi.org/10.1021/acsmedchemlett.8b00464openalex-snapshot
Inhibition of PCSK9D374Y/LDLR Protein–Protein Interaction by Computationally Designed T9 Lupin Peptide
inferred← citeshttps://doi.org/10.1021/acsomega.6b00086openalex-snapshot
Predicting Binding Affinities for GPCR Ligands Using Free-Energy Perturbation
inferred← citeshttps://doi.org/10.1021/acsomega.8b03258openalex-snapshot
Effective Estimation of Ligand-Binding Affinity Using Biased Sampling Method
inferred← citeshttps://doi.org/10.1021/ci5004027openalex-snapshot
A Large-Scale Test of Free-Energy Simulation Estimates of Protein–Ligand Binding Affinities
inferred← citeshttps://doi.org/10.1021/ja512751qopenalex-snapshot
Accurate and Reliable Prediction of Relative Ligand Binding Potency in Prospective Drug Discovery by Way of a Modern Free-Energy Calculation Protocol and Force Field
inferred← citeshttps://doi.org/10.1021/jacs.7b08938openalex-snapshot
Can Relative Binding Free Energy Predict Selectivity of Reversible Covalent Inhibitors?
inferred← citeshttps://doi.org/10.1021/jacsau.3c00725openalex-snapshot
Molecular Mechanisms Underlying Medium-Chain Free Fatty Acid-Regulated Activity of the Phospholipase PlaF from Pseudomonas aeruginosa
inferred← citeshttps://doi.org/10.1038/s41598-018-23039-5openalex-snapshot
Predicting Binding Free Energies of PDE2 Inhibitors. The Difficulties of Protein Conformation
inferred← citeshttps://doi.org/10.1038/s41598-018-33050-5openalex-snapshot
Hydrophobic alkyl chains substituted to the 8-position of cyclic nucleotides enhance activation of CNG and HCN channels by an intricate enthalpy - entropy compensation
inferred← citeshttps://doi.org/10.1038/s41598-018-35819-0openalex-snapshot
Biological Characterization of Computationally Designed Analogs of peptide TVFTSWEEYLDWV (Pep2-8) with Increased PCSK9 Antagonistic Activity
inferred← citeshttps://doi.org/10.1038/s41598-019-46496-yopenalex-snapshot
Isoform-specific Inhibition of N-methyl-D-aspartate Receptors by Bile Salts
inferred← citeshttps://doi.org/10.1038/s41598-020-68134-8openalex-snapshot
Design, synthesis, structure, in vitro cytotoxic activity evaluation and docking studies on target enzyme GSK-3β of new indirubin-3ʹ-oxime derivatives
inferred← citeshttps://doi.org/10.1039/d0ra06212jopenalex-snapshot
Rapid prediction of possible inhibitors for SARS-CoV-2 main protease using docking and FPL simulations
inferred← citeshttps://doi.org/10.1039/d0ra06675copenalex-snapshot
Pharmacoinformatics approaches to identify potential hits against tetraacyldisaccharide 4′-kinase (LpxK) of Pseudomonas aeruginosa
inferred← citeshttps://doi.org/10.1039/d0ra09858bopenalex-snapshot
Binding of inhibitors to the monomeric and dimeric SARS-CoV-2 Mpro
inferred← citeshttps://doi.org/10.1039/d1ra01855hopenalex-snapshot
Molecular design of anticancer drugs from marine fungi derivatives
inferred← citeshttps://doi.org/10.1039/d1ra02529eopenalex-snapshot
Computational estimation of potential inhibitors from known drugs against the main protease of SARS-CoV-2
inferred← citeshttps://doi.org/10.1039/d1ra06534copenalex-snapshot
Searching and designing potential inhibitors for SARS-CoV-2 Mpro from natural sources using atomistic and deep-learning calculations
inferred← citeshttps://doi.org/10.1039/d2cp04476eopenalex-snapshot
Characterizing the ligand-binding affinity toward SARS-CoV-2 Mpro via physics- and knowledge-based approaches
inferred← citeshttps://doi.org/10.1039/d4ra00692eopenalex-snapshot
Alchemical approach performance in calculating the ligand-binding free energy
inferred← citeshttps://doi.org/10.1039/d5cs00415bopenalex-snapshot
Modeling protein–ligand interactions for drug discovery in the era of deep learning
inferred← citeshttps://doi.org/10.1063/1.5123154openalex-snapshot
Perturbation potentials to overcome order/disorder transitions in alchemical binding free energy calculations
inferred← citeshttps://doi.org/10.1063/1674-0068/30/cjcp1711204openalex-snapshot
Comparison of Accuracy and Convergence Rate between Equilibrium and Nonequilibrium Alchemical Transformations for Calculation of Relative Binding Free Energy
inferred← citeshttps://doi.org/10.1070/rcr5001openalex-snapshot
Photopharmacological compounds based on azobenzenes and azoheteroarenes: principles of molecular design, molecular modelling, and synthesis
inferred← citeshttps://doi.org/10.1080/07391102.2019.1666745openalex-snapshot
Evaluation of pyrazolopyrimidine derivatives as microtubule affinity regulating kinase 4 inhibitors: Towards therapeutic management of Alzheimer’s disease
inferred← citeshttps://doi.org/10.1080/07391102.2020.1868335openalex-snapshot
Fisetin 8-C-glucoside as entry inhibitor in SARS CoV-2 infection: molecular modelling study
inferred← citeshttps://doi.org/10.1080/07391102.2021.1885496openalex-snapshot
Evaluation of binding of potential ADMET/tox screened saquinavir analogues for inhibition of HIV-protease via molecular dynamics and binding free energy calculations
inferred← citeshttps://doi.org/10.1080/07391102.2023.2214209openalex-snapshot
Integrated molecular modeling and dynamics approaches revealed potential natural inhibitors of NF-κB transcription factor as breast cancer therapeutics
inferred← citeshttps://doi.org/10.1080/07391102.2023.2226737openalex-snapshot
Exploring binding modes of the selected inhibitors to SND1 by all-atom molecular dynamics simulations
inferred← citeshttps://doi.org/10.1080/07391102.2023.2263588openalex-snapshot
Structure-based virtual screening of natural compounds as inhibitors of HCV using molecular docking and molecular dynamics simulation studies
inferred← citeshttps://doi.org/10.1080/07391102.2024.2321509openalex-snapshot
Natural compounds inhibit Monkeypox virus methyltransferase VP39 in silico studies
inferred← citeshttps://doi.org/10.1080/07391102.2025.2475222openalex-snapshot
Molecular mechanism of ZER1-mediated recognition of N-terminal glycine in protein degradation
inferred← citeshttps://doi.org/10.1080/10799893.2024.2405488openalex-snapshot
Virtual screening, molecular docking and dynamics simulation studies to identify potential agonists of orphan receptor GPR78 targeting CNS disorders
inferred← citeshttps://doi.org/10.1098/rsfs.2020.0007openalex-snapshot
Rapid, accurate, precise and reproducible ligand–protein binding free energy prediction
inferred← citeshttps://doi.org/10.1101/2020.08.25.267625openalex-snapshot
MMGB/SA Consensus Estimate of the Binding Free Energy Between the Novel Coronavirus Spike Protein to the Human ACE2 Receptor
inferred← citeshttps://doi.org/10.1101/333120openalex-snapshot
Effect of set up protocols on the accuracy of alchemical free energy calculation over a set of ACK1 inhibitors
inferred← citeshttps://doi.org/10.1105/tpc.19.00406openalex-snapshot
Posttranslational Modification of the NADP-Malic Enzyme Involved in C 4 Photosynthesis Modulates the Enzymatic Activity during the Day
inferred← citeshttps://doi.org/10.1111/cbdd.13147openalex-snapshot
In silico ligand‐based modeling of hBACE ‐1 inhibitors
inferred← citeshttps://doi.org/10.1111/cbdd.13347openalex-snapshot
An attempt to incorporate effect of direct interaction between a ligand and explicit water molecules into MM /3D‐ RISM
inferred← citeshttps://doi.org/10.1111/cbdd.13446openalex-snapshot
Suitability of MMGBSA for the selection of correct ligand binding modes from docking results
inferred← citeshttps://doi.org/10.1142/s021972002250024xopenalex-snapshot
The impact of simulation time in predicting binding free energies using end-point approaches
inferred← citeshttps://doi.org/10.1142/s2737416523500242openalex-snapshot
Designing Potential Inhibitors of SARS-CoV-2 Mpro Using Deep Learning and Steered Molecular Dynamic Simulations
inferred← citeshttps://doi.org/10.1145/3388440.3414712openalex-snapshot
Binding Free Energy of the Novel Coronavirus Spike Protein and the Human ACE2 Receptor
inferred← citeshttps://doi.org/10.1146/annurev-biophys-070816-033654openalex-snapshot
Predicting Binding Free Energies: Frontiers and Benchmarks
inferred← citeshttps://doi.org/10.1155/bri/7191508openalex-snapshot
In Silico Bioprospection of Daniellia oliveri– Based Products as Quorum Sensing Modulators of Escherichia coli SdiA
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1004693openalex-snapshot
Molecular Mechanisms of Glutamine Synthetase Mutations that Lead to Clinically Relevant Pathologies
inferred← citeshttps://doi.org/10.1371/journal.pone.0177907openalex-snapshot
The structural basis of a high affinity ATP binding ε subunit from a bacterial ATP synthase
inferred← citeshttps://doi.org/10.1371/journal.pone.0207673openalex-snapshot
Features of interactions responsible for antifungal activity against resistant type cytochrome bc1: A data-driven analysis based on the binding free energy at the atomic level
inferred← citeshttps://doi.org/10.1371/journal.pone.0213217openalex-snapshot
Effect of set up protocols on the accuracy of alchemical free energy calculation over a set of ACK1 inhibitors
inferred← citeshttps://doi.org/10.1517/17460441.2015.1032936openalex-snapshot
The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities
inferred← citeshttps://doi.org/10.21203/rs.3.rs-1046506/v1openalex-snapshot
Molecular Dynamics Free Energy Simulation study to Investigate Binding Pattern of Isoliquiritigenin as PPAR𝛾 Agonist
inferred← citeshttps://doi.org/10.26434/chemrxiv-2023-llhdqopenalex-snapshot
A Computational Workflow for Refining AF2 Models in Drug Design Using Kinetic and Thermodynamic Binding Calculations: A Case Study for the Unresolved Inactive human Adenosine A3 Receptor
inferred← citeshttps://doi.org/10.26434/chemrxiv.12616370.v1openalex-snapshot
Rapid Prediction of Possible Inhibitors for SARS-CoV-2 Main Protease using Docking and FPL Simulations
inferred← citeshttps://doi.org/10.26434/chemrxiv.13318523openalex-snapshot
A Benchmark of Popular Free Energy Approaches Revealing the Inhibitors Binding to SARS-CoV2 Mpro
inferred← citeshttps://doi.org/10.26434/chemrxiv.14102675openalex-snapshot
Computational Estimation of Potential Inhibitors from the Known Drugs against the Main Protease of SARS-CoV-2
inferred← citeshttps://doi.org/10.26434/chemrxiv.8967944openalex-snapshot
Structural Characterization of Agonist Binding to A3 Adenosine Receptor through Biomolecular Simulations and Mutagenesis Experiments
inferred← citeshttps://doi.org/10.3389/fmolb.2020.00106openalex-snapshot
On Calculating Free Energy Differences Using Ensembles of Transition Paths
inferred← citeshttps://doi.org/10.3389/fmolb.2022.972162openalex-snapshot
Assessing the effect of forcefield parameter sets on the accuracy of relative binding free energy calculations
inferred← citeshttps://doi.org/10.3389/frai.2024.1398126openalex-snapshot
Advancing smart city factories: enhancing industrial mechanical operations via deep learning techniques
inferred← citeshttps://doi.org/10.3390/cimb48040404openalex-snapshot
Identification of Potential Pancreatic Lipase Inhibitors from Traditional Chinese Medicines via Molecular Docking, Molecular Dynamics Simulation and In Vitro Validation
inferred← citeshttps://doi.org/10.3390/ijms21134765openalex-snapshot
Absolute Binding Free Energy Calculations for Highly Flexible Protein MDM2 and Its Inhibitors
inferred← citeshttps://doi.org/10.3390/ijms22063078openalex-snapshot
Accurate Receptor-Ligand Binding Free Energies from Fast QM Conformational Chemical Space Sampling
inferred← citeshttps://doi.org/10.3390/molecules26082383openalex-snapshot
An Effective MM/GBSA Protocol for Absolute Binding Free Energy Calculations: A Case Study on SARS-CoV-2 Spike Protein and the Human ACE2 Receptor
inferred← citeshttps://doi.org/10.3390/ph15080984openalex-snapshot
Total Synthesis of the Antimycobacterial Natural Product Chlorflavonin and Analogs via a Late-Stage Ruthenium(II)-Catalyzed ortho-C(sp2)-H-Hydroxylation
inferred← citeshttps://doi.org/10.3390/pharmaceutics14030665openalex-snapshot
Computational Design and Biological Evaluation of Analogs of Lupin Peptide P5 Endowed with Dual PCSK9/HMG-CoAR Inhibiting Activity
inferred← citeshttps://doi.org/10.64898/2026.06.15.732264openalex-snapshot
Chitinase-3-like protein 1 decodes chitosan acetylation patterns into toll-like receptor 2 signaling through heparan sulfate
inferred← citeshttps://doi.org/10.70675/a996b680z03d4z4794z8495zc0d7f055f272openalex-snapshot
Computational approaches to molecular recognition : from host-guest to protein-ligand binding
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