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A comprehensive examination of the contributions to the binding entropy of protein–ligand complexes
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Systematic analysis of domain motions in proteins from conformational change: New results on citrate synthase and T4 lysozyme
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Domain motions in bacteriophage T4 lysozyme: A comparison between molecular dynamics and crystallographic data
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Energy landscape of a native protein: Jumping-among-minima model
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Examining methods for calculations of binding free energies: LRA, LIE, PDLD-LRA, and PDLD/S-LRA calculations of ligands binding to an HIV protease
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Approaches to the Description and Prediction of the Binding Affinity of Small-Molecule Ligands to Macromolecular Receptors
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Advances in Enzymology and Related Areas of Molecular Biology
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Binding Energy, Specificity, and Enzymic Catalysis: The Circe Effect
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Thermodynamic Inhibition Profile of a Cyclopentyl and a Cyclohexyl Derivative towards Thrombin: The Same but for Different Reasons
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Predicting Drug‐Resistant Mutations of HIV Protease
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Can the calculation of ligand binding free energies be improved with continuum solvent electrostatics and an ideal‐gas entropy correction?
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Converging free energy estimates: MM‐PB(GB)SA studies on the protein–protein complex Ras–Raf
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Microscopic and semimicroscopic calculations of electrostatic energies in proteins by the POLARIS and ENZYMIX programs
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A preference-based free-energy parameterization of enzyme-inhibitor binding. Applications to HIV-1-protease inhibitor design
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Contributions to the binding free energy of ligands to avidin and streptavidin
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Absolute binding free energy calculations: On the accuracy of computational scoring of protein–ligand interactions
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The Contribution of Vibrational Entropy to Molecular Association
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Electrostatic and non-electrostatic contributions to the binding free energies of anthracycline antibiotics to DNA
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Factorising ligand affinity: a combined thermodynamic and crystallographic study of trypsin and thrombin inhibition†
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Scoring noncovalent protein-ligand interactions: A continuous differentiable function tuned to compute binding affinities
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LUDI: rule-based automatic design of new substituents for enzyme inhibitor leads
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The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure
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Co-operativity in protein-protein association
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Do enthalpy and entropy distinguish first in class from best in class?
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Halogenated Benzenes Bound within a Non-polar Cavity in T4 Lysozyme Provide Examples of I⋯S and I⋯Se Halogen-bonding
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Revisiting Free Energy Calculations: A Theoretical Connection to MM/PBSA and Direct Calculation of the Association Free Energy
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The statistical-thermodynamic basis for computation of binding affinities: a critical review
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Normal mode analysis of protein dynamics
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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
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Extracting hydrophobic free energies from experimental data: relationship to protein folding and theoretical models
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Role of hydrophobicity in the binding of coenzymes
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On the Interpretation of the Observed Linear Free Energy Relationship in Phosphate Hydrolysis: A Thorough Computational Study of Phosphate Diester Hydrolysis in Solution
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Information Theory-Based Scoring Function for the Structure-Based Prediction of Protein−Ligand Binding Affinity
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Harmonic and quasiharmonic descriptions of crambin
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Inclusion of Loss of Translational and Rotational Freedom in Theoretical Estimates of Free Energies of Binding. Application to a Complex of Benzene and Mutant T4 Lysozyme
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Continuum Solvent Studies of the Stability of DNA, RNA, and Phosphoramidate−DNA Helices
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Synthetic Adenine Receptors: Direct Calculation of Binding Affinity and Entropy
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Binding of a Diverse Set of Ligands to Avidin and Streptavidin: An Accurate Quantitative Prediction of Their Relative Affinities by a Combination of Molecular Mechanics and Continuum Solvent Models
inferredcites →https://doi.org/10.1021/jm980536jopenalex-snapshot
A General and Fast Scoring Function for Protein−Ligand Interactions: A Simplified Potential Approach
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Calculations of Activation Entropies of Chemical Reactions in Solution
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Absolute and Relative Entropies from Computer Simulation with Applications to Ligand Binding
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Toward Accurate Microscopic Calculation of Solvation Entropies: Extending the Restraint Release Approach to Studies of Solvation Effects
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Consistent Calculations of pKa's of Ionizable Residues in Proteins: Semi-microscopic and Microscopic Approaches
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Method for estimating the configurational entropy of macromolecules
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Ligand binding affinity prediction by linear interaction energy methods
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Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes
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Prediction of binding constants of protein ligands: A fast method for the prioritization of hits obtained from de novo design or 3D database search programs
inferredcites →https://doi.org/10.1023/a:1008040323669openalex-snapshot
Empirical scoring functions. II. The testing of an empirical scoring function for the prediction of ligand-receptor binding affinities and the use of Bayesian regression to improve the quality of the model
inferredcites →https://doi.org/10.1023/a:1022446720849openalex-snapshot
The consequences of translational and rotational entropy lost by small molecules on binding to proteins
inferredcites →https://doi.org/10.1038/nature03197openalex-snapshot
Virtual screening of chemical libraries
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Calculations of solute and solvent entropies from molecular dynamics simulations
inferredcites →https://doi.org/10.1039/p29950000141openalex-snapshot
Application of a generalised enthalpy–entropy relationship to binding co-operativity and weak associations in solution
inferredcites →https://doi.org/10.1046/j.1432-1033.2001.01991.xopenalex-snapshot
Thermodynamic analysis of binding of p-substituted benzamidines to trypsin
inferredcites →https://doi.org/10.1073/pnas.0405573101openalex-snapshot
Bulk-solvent and hydration-shell fluctuations, similar to α- and β-fluctuations in glasses, control protein motions and functions
inferredcites →https://doi.org/10.1073/pnas.162365999openalex-snapshot
On the calculation of absolute macromolecular binding free energies
inferredcites →https://doi.org/10.1073/pnas.68.8.1678openalex-snapshot
Entropic Contributions to Rate Accelerations in Enzymic and Intramolecular Reactions and the Chelate Effect
inferredcites →https://doi.org/10.1093/protein/12.3.185openalex-snapshot
Comment on: `The entropy cost of protein association'
inferredcites →https://doi.org/10.1093/protein/5.3.215openalex-snapshot
Calculations of antibody-antigen interactions: microscopic and semi-microscopic evaluation of the free energies of binding of phosphorylcholine analogs to McPC603
inferredcites →https://doi.org/10.1093/protein/8.11.1137openalex-snapshot
Estimation of binding free energies for HIV proteinase inhibitors by molecular dynamics simulations
inferredcites →https://doi.org/10.1111/j.1747-0285.2005.00314.xopenalex-snapshot
Overcoming Roadblocks in Lead Optimization: A Thermodynamic Perspective
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Biomolecular Simulations: Recent Developments in Force Fields, Simulations of Enzyme Catalysis, Protein-Ligand, Protein-Protein, and Protein-Nucleic Acid Noncovalent Interactions
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Molecular Recognition and Docking Algorithms
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Calorimetry and Thermodynamics in Drug Design
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Entropy Calculation of HIV-1 Env gp120, its Receptor CD4, and their Complex: An Analysis of Configurational Entropy Changes upon Complexation
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Incoming claims: where this work appears in other papers’ reference lists and arguments.
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