Spatial analysis and quantification of the thermodynamic driving forces in protein-ligand binding: binding site variability

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Spatial analysis and quantification of the thermodynamic driving forces in protein-ligand binding: binding site variability is …
instance of (P31):
scholarly articleQ13442814

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P356DOI10.1021/JA512054F
P3181OpenCitations bibliographic resource ID4460912
P932PMC publication ID4342289
P698PubMed publication ID25625202
P5875ResearchGate publication ID271593616

P50authorAlex MacKerellQ57907659
P2093author name stringE Prabhu Raman
P2860cites workEfficient calculation of configurational entropy from molecular simulations by combining the mutual-information expansion and nearest-neighbor methodsQ23923380
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Water in cavity-ligand recognitionQ24618521
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Structural basis for p38alpha MAP kinase quinazolinone and pyridol-pyrimidine inhibitor specificityQ27641774
Mechanism of the hydrophobic effect in the biomolecular recognition of arylsulfonamides by carbonic anhydraseQ27675123
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Comparing distance metrics for rotation using the k-nearest neighbors algorithm for entropy estimationQ28397929
Computational fragment-based binding site identification by ligand competitive saturationQ28475699
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Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulationsQ29547631
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Sampling of Organic Solutes in Aqueous and Heterogeneous Environments Using Oscillating Excess Chemical Potentials in Grand Canonical-like Monte Carlo-Molecular Dynamics SimulationsQ40572087
Site-Specific Fragment Identification Guided by Single-Step Free Energy Perturbation CalculationsQ41451646
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Calculation of Standard Binding Free Energies:  Aromatic Molecules in the T4 Lysozyme L99A Mutant.Q53190267
Hydration in drug design. 3. Conserved water molecules at the ligand-binding sites of homologous proteins.Q53903013
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Evaluation of Host-Guest Binding Thermodynamics of Model Cavities with Grid Cell TheoryQ86750030
P433issue7
P407language of work or nameEnglishQ1860
P921main subjectcatalysisQ82264
ligand bindingQ61659151
P304page(s)2608-2621
P577publication date2015-02-16
P1433published inJournal of the American Chemical SocietyQ898902
P1476titleSpatial analysis and quantification of the thermodynamic driving forces in protein-ligand binding: binding site variability
P478volume137

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cites work (P2860)
Q51304233AutoDock-GIST: Incorporating Thermodynamics of Active-Site Water into Scoring Function for Accurate Protein-Ligand Docking.
Q37565935Driving Structure-Based Drug Discovery through Cosolvent Molecular Dynamics
Q41099155Enthalpic and Entropic Contributions to Hydrophobicity
Q90267981Free Energies and Entropies of Binding Sites Identified by MixMD Cosolvent Simulations
Q41512122Hot-spot identification on a broad class of proteins and RNA suggest unifying principles of molecular recognition.
Q47245406Predicting Displaceable Water Sites Using Mixed-Solvent Molecular Dynamics
Q41818888Quantitative Correlation of Conformational Binding Enthalpy with Substrate Specificity of Serine Proteases
Q46202746Solvation Structure and Thermodynamic Mapping (SSTMap): An Open-Source, Flexible Package for the Analysis of Water in Molecular Dynamics Trajectories.
Q48049114Solvent effects on ligand binding to a serine protease

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