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Using Free Energy of Binding Calculations To Improve the Accuracy of Virtual Screening Predictions
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Outgoing claims: the papers this work cites, builds on, or argues with.
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Evaluation of the FLEXX incremental construction algorithm for protein-ligand docking
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Evaluation of library ranking efficacy in virtual screening
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A semiempirical free energy force field with charge‐based desolvation
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AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility
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Drug efficiency indices for improvement of molecular docking scoring functions
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CHARMM : A program for macromolecular energy, minimization, and dynamics calculations
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Combining docking and molecular dynamic simulations in drug design
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Principles of docking: An overview of search algorithms and a guide to scoring functions
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Development and validation of a modular, extensible docking program: DOCK 5
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Structure-based discovery of dengue virus protease inhibitors
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Structure-based virtual screening of Src kinase inhibitors
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Identification of novel serotonin 2C receptor ligands by sequential virtual screening
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Discovery of 3-(4-bromophenyl)-6-nitrobenzo[1.3.2]dithiazolium ylide 1,1-dioxide as a novel dual cyclooxygenase/5-lipoxygenase inhibitor that also inhibits tumor necrosis factor-α production
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Identification of small molecules that inhibit GSK-3β through virtual screening
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Virtual screening to identify lead inhibitors for bacterial NAD synthetase (NADs)
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Identification of a novel inhibitor of JAK2 tyrosine kinase by structure-based virtual screening
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Structure-based virtual screening of chemical libraries for drug discovery
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Predicting Absolute Ligand Binding Free Energies to a Simple Model Site
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Automatic atom type and bond type perception in molecular mechanical calculations
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Identification of potent urease inhibitors via ligand- and structure-based virtual screening and in vitro assays
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Flexible ligand docking to multiple receptor conformations: a practical alternative
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The statistical-thermodynamic basis for computation of binding affinities: a critical review
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Consensus scoring for ligand/protein interactions
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Calculating Structures and Free Energies of Complex Molecules: Combining Molecular Mechanics and Continuum Models
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Energetic origins of specificity of ligand binding in an interior nonpolar cavity of T4 lysozyme
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Specificity of ligand binding in a buried nonpolar cavity of T4 lysozyme: Linkage of dynamics and structural plasticity
inferredcites →https://doi.org/10.1021/ct060037vopenalex-snapshot
Calculation of Standard Binding Free Energies: Aromatic Molecules in the T4 Lysozyme L99A Mutant
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Confine-and-Release Method: Obtaining Correct Binding Free Energies in the Presence of Protein Conformational Change
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Computational Alchemy To Calculate Absolute Protein−Ligand Binding Free Energy
inferredcites →https://doi.org/10.1021/jm0306430openalex-snapshot
Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy
inferredcites →https://doi.org/10.1021/jm049798dopenalex-snapshot
Comparison of Automated Docking Programs as Virtual Screening Tools
inferredcites →https://doi.org/10.1021/jm050362nopenalex-snapshot
A Critical Assessment of Docking Programs and Scoring Functions
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Prediction of Protein−Ligand Interactions. Docking and Scoring: Successes and Gaps
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Discovery of Novel Fibroblast Growth Factor Receptor 1 Kinase Inhibitors by Structure-Based Virtual Screening
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Consensus Scoring: A Method for Obtaining Improved Hit Rates from Docking Databases of Three-Dimensional Structures into Proteins
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Absolute Binding Free Energies: A Quantitative Approach for Their Calculation
inferredcites →https://doi.org/10.1021/jp807701hopenalex-snapshot
Computations of Standard Binding Free Energies with Molecular Dynamics Simulations
inferredcites →https://doi.org/10.1021/jp973084fopenalex-snapshot
All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins
inferredcites →https://doi.org/10.1023/b:jcam.0000017496.76572.6fopenalex-snapshot
Comparative study of several algorithms for flexible ligand docking
inferredcites →https://doi.org/10.1038/355371a0openalex-snapshot
A cavity-containing mutant of T4 lysozyme is stabilized by buried benzene
inferredcites →https://doi.org/10.1038/nrd1549openalex-snapshot
Docking and scoring in virtual screening for drug discovery: methods and applications
inferredcites →https://doi.org/10.1063/1.2221683openalex-snapshot
On the use of orientational restraints and symmetry corrections in alchemical free energy calculations
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Computation of binding free energy with molecular dynamics and grand canonical Monte Carlo simulations
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Efficient computation of absolute free energies of binding by computer simulations. Application to the methane dimer in water
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A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions
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Cooperative water filling of a nonpolar protein cavity observed by high-pressure crystallography and simulation
inferredcites →https://doi.org/10.1146/annurev.biophys.36.040306.132550openalex-snapshot
Calculation of Protein-Ligand Binding Affinities
inferredcites →https://doi.org/10.1529/biophysj.106.084301openalex-snapshot
Absolute Binding Free Energy Calculations Using Molecular Dynamics Simulations with Restraining Potentials
inferredcites →https://doi.org/10.2174/1381612033454595openalex-snapshot
Conformational Flexibility Models for the Receptor in Structure Based Drug Design
inferredcites →https://doi.org/10.2174/1386207013330661openalex-snapshot
The Linear Interaction Energy Method for Predicting Ligand Binding Free Energies
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New Approaches to Structure-Based Discovery of Dengue Protease Inhibitors
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Detailed Comparison of the Protein-Ligand Docking Efficiencies of GOLD, a Commercial Package and ArgusLab, a Licensable Freeware
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CURRENT PROGRESS IN STRUCTURE-BASED RATIONAL DRUG DESIGN MARKS A NEW MINDSET IN DRUG DISCOVERY
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