Free energy, entropy, and induced fit in host-guest recognition: calculations with the second-generation mining minima algorithm.
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Insights into Protein-Ligand Interactions: Mechanisms, Models, and MethodsRescoring Docking Hit Lists for Model Cavity Sites: Predictions and Experimental TestingPredicting Ligand Binding Affinity with Alchemical Free Energy Methods in a Polar Model Binding SiteEngineering a model protein cavity to catalyze the Kemp eliminationInvestigation of Carbohydrate Recognition via Computer SimulationTheory of free energy and entropy in noncovalent bindingDevelop and test a solvent accessible surface area-based model in conformational entropy calculationsExtending fragment-based free energy calculations with library Monte Carlo simulation: annealing in interaction spaceMolecular modeling of nucleic acid structure: energy and samplingAccelerated convergence of molecular free energy via superposition approximation-based reference statesEfficient calculation of molecular configurational entropies using an information theoretic approximationEfficient Computation of Small-Molecule Configurational Binding Entropy and Free Energy Changes by Ensemble EnumerationConfigurational entropy in protein-peptide binding: computational study of Tsg101 ubiquitin E2 variant domain with an HIV-derived PTAP nonapeptideCharacterization of Promiscuous Binding of Phosphor Ligands to Breast-Cancer-Gene 1 (BRCA1) C-Terminal (BRCT): Molecular Dynamics, Free Energy, Entropy and Inhibitor DesignExtraction of configurational entropy from molecular simulations via an expansion approximationExhaustive docking and solvated interaction energy scoring: lessons learned from the SAMPL4 challenge.Parameterization of an effective potential for protein-ligand binding from host-guest affinity data.Polar solvent effects on tartaric acid binding by aromatic oligoamide foldamer capsules.A black-box re-weighting analysis can correct flawed simulation dataVirtual ligand screening against Escherichia coli dihydrofolate reductase: improving docking enrichment using physics-based methods.Absolute free energies estimated by combining precalculated molecular fragment librariesThe SAMPL4 host-guest blind prediction challenge: an overview.Understanding ligand-receptor non-covalent binding kinetics using molecular modeling.Entropy-enthalpy compensation: role and ramifications in biomolecular ligand recognition and design.Modeling the pharmacodynamics of passive membrane permeabilityLarge scale affinity calculations of cyclodextrin host-guest complexes: Understanding the role of reorganization in the molecular recognition process.Accurate prediction of the binding free energy and analysis of the mechanism of the interaction of replication protein A (RPA) with ssDNA.Calculation of cyclodextrin binding affinities: energy, entropy, and implications for drug design.Prediction of SAMPL3 host-guest binding affinities: evaluating the accuracy of generalized force-fields.Blind prediction of host-guest binding affinities: a new SAMPL3 challenge.The Binding Energy Distribution Analysis Method (BEDAM) for the Estimation of Protein-Ligand Binding Affinities.Probing molecular docking in a charged model binding site.New ultrahigh affinity host-guest complexes of cucurbit[7]uril with bicyclo[2.2.2]octane and adamantane guests: thermodynamic analysis and evaluation of M2 affinity calculationsSymmetry numbers for rigid, flexible, and fluxional molecules: theory and applicationsEfficient incorporation of protein flexibility and dynamics into molecular docking simulationsSolvent interaction energy calculations on molecular dynamics trajectories: increasing the efficiency using systematic frame selection.Ligand configurational entropy and protein binding.Conformational Transitions and Convergence of Absolute Binding Free Energy Calculations.Statistical mechanics and molecular dynamics in evaluating thermodynamic properties of biomolecular recognition.Molecular evolution of affinity and flexibility in the immune system.
P2860
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P2860
Free energy, entropy, and induced fit in host-guest recognition: calculations with the second-generation mining minima algorithm.
description
2004 nî lūn-bûn
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2004年の論文
@ja
2004年学术文章
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2004年学术文章
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2004年学术文章
@zh-cn
2004年学术文章
@zh-hans
2004年学术文章
@zh-my
2004年学术文章
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2004年學術文章
@zh-hant
name
Free energy, entropy, and indu ...... ation mining minima algorithm.
@en
Free energy, entropy, and indu ...... ation mining minima algorithm.
@nl
type
label
Free energy, entropy, and indu ...... ation mining minima algorithm.
@en
Free energy, entropy, and indu ...... ation mining minima algorithm.
@nl
prefLabel
Free energy, entropy, and indu ...... ation mining minima algorithm.
@en
Free energy, entropy, and indu ...... ation mining minima algorithm.
@nl
P356
P1476
Free energy, entropy, and indu ...... ation mining minima algorithm.
@en
P2093
Chia-En Chang
Michael K Gilson
P304
13156-13164
P356
10.1021/JA047115D
P407
P577
2004-10-01T00:00:00Z