Computations of standard binding free energies with molecular dynamics simulations.
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Computational analysis of phosphopeptide binding to the polo-box domain of the mitotic kinase PLK1 using molecular dynamics simulationEnhanced conformational sampling to visualize a free-energy landscape of protein complex formationInsights into Protein-Ligand Interactions: Mechanisms, Models, and MethodsComputational drug design strategies applied to the modelling of human immunodeficiency virus-1 reverse transcriptase inhibitorsComputational studies of marine toxins targeting ion channelsRational approaches to improving selectivity in drug designThermophilic proteins: insight and perspective from in silico experimentsGaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy CalculationCrystal structure of the deglycating enzyme Amadoriase I in its free form and substrate-bound complexAbsolute free energy of binding of avidin/biotin, revisitedExtending fragment-based free energy calculations with library Monte Carlo simulation: annealing in interaction spaceCalculation of the Absolute Free Energy of Binding and Related Entropies with the HSMD-TI Method: The FKBP12-L8 ComplexInterrogation of the protein-protein interactions between human BRCA2 BRC repeats and RAD51 reveals atomistic determinants of affinityLocating the route of entry and binding sites of benzocaine and phenytoin in a bacterial voltage gated sodium channelInsight on Mutation-Induced Resistance from Molecular Dynamics Simulations of the Native and Mutated CSF-1R and KITComputational prediction of metabolism: sites, products, SAR, P450 enzyme dynamics, and mechanismsProtein-Ligand Electrostatic Binding Free Energies from Explicit and Implicit SolvationComputational protein design: the Proteus software and selected applications.A Python tool to set up relative free energy calculations in GROMACS.Guidelines for the analysis of free energy calculationsBringing Clarity to the Prediction of Protein-Ligand Binding Free Energies via "Blurring"Computational analysis of membrane proteins: the largest class of drug targets.CrystalDock: a novel approach to fragment-based drug design.Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamics.Lead optimization mapper: automating free energy calculations for lead optimization.Alchemical free energy methods for drug discovery: progress and challengesProbing carbohydrate product expulsion from a processive cellulase with multiple absolute binding free energy methods.Identifying low variance pathways for free energy calculations of molecular transformations in solution phase.Optimal pairwise and non-pairwise alchemical pathways for free energy calculations of molecular transformation in solution phase.Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations.Funnel metadynamics as accurate binding free-energy methodStandard binding free energies from computer simulations: What is the best strategy?In silico-based vaccine design against Ebola virus glycoproteinCorrect folding of an α-helix and a β-hairpin using a polarized 2D torsional potential.Flexibility and binding affinity in protein-ligand, protein-protein and multi-component protein interactions: limitations of current computational approaches.Computational analysis of the binding specificity of Gleevec to Abl, c-Kit, Lck, and c-Src tyrosine kinases.The cis conformation of proline leads to weaker binding of a p53 peptide to MDM2 compared to trans.Recent trends and observations in the design of high-quality screening collections.Relative Binding Enthalpies from Molecular Dynamics Simulations Using a Direct Method.Using free energy of binding calculations to improve the accuracy of virtual screening predictions.
P2860
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P2860
Computations of standard binding free energies with molecular dynamics simulations.
description
article científic
@ca
article scientifique
@fr
articolo scientifico
@it
artigo científico
@pt
bilimsel makale
@tr
scientific article published on February 2009
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vedecký článok
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vetenskaplig artikel
@sv
videnskabelig artikel
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vědecký článek
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name
Computations of standard binding free energies with molecular dynamics simulations.
@en
Computations of standard binding free energies with molecular dynamics simulations.
@nl
type
label
Computations of standard binding free energies with molecular dynamics simulations.
@en
Computations of standard binding free energies with molecular dynamics simulations.
@nl
prefLabel
Computations of standard binding free energies with molecular dynamics simulations.
@en
Computations of standard binding free energies with molecular dynamics simulations.
@nl
P2860
P356
P1476
Computations of standard binding free energies with molecular dynamics simulations.
@en
P2093
Benoît Roux
Yuqing Deng
P2860
P304
P356
10.1021/JP807701H
P407
P577
2009-02-01T00:00:00Z