On the use of orientational restraints and symmetry corrections in alchemical free energy calculations
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Predicting absolute ligand binding free energies to a simple model siteRapid Heme Transfer Reactions between NEAr Transporter Domains of Staphylococcus aureus: A Theoretical Study Using QM/MM and MD SimulationsPredicting Ligand Binding Affinity with Alchemical Free Energy Methods in a Polar Model Binding SiteA crystallographic and modelling study of a human telomeric RNA (TERRA) quadruplexBlind Prediction of Charged Ligand Binding Affinities in a Model Binding SiteCalculation and visualization of atomistic mechanical stresses in nanomaterials and biomoleculesACPYPE - AnteChamber PYthon Parser interfacEModeling of arylamide helix mimetics in the p53 peptide binding site of hDM2 suggests parallel and anti-parallel conformations are both stable.Dodecyl maltoside protects membrane proteins in vacuo.Computing the relative stabilities and the per-residue components in protein conformational changes.Bringing Clarity to the Prediction of Protein-Ligand Binding Free Energies via "Blurring"The Confine-and-Release Method: Obtaining Correct Binding Free Energies in the Presence of Protein Conformational ChangeNuclear magnetic resonance signal chemical shifts and molecular simulations: a multidisciplinary approach to modeling copper protein structures.Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamics.Assessment of protein structure refinement in CASP9.Perspective: Alchemical free energy calculations for drug discovery.Alchemical free energy methods for drug discovery: progress and challengesProbing carbohydrate product expulsion from a processive cellulase with multiple absolute binding free energy methods.Assessing the performance of MM/PBSA and MM/GBSA methods. 4. Accuracies of MM/PBSA and MM/GBSA methodologies evaluated by various simulation protocols using PDBbind data set.Computational study of evolutionary selection pressure on rainbow trout estrogen receptors.Hydration Free Energy from Orthogonal Space Random Walk and Polarizable Force Field.Using free energy of binding calculations to improve the accuracy of virtual screening predictions.GROMACS molecule & liquid database.Cupricyclins, novel redox-active metallopeptides based on conotoxins scaffold.The Binding Energy Distribution Analysis Method (BEDAM) for the Estimation of Protein-Ligand Binding Affinities.Computing Relative Free Energies of Solvation using Single Reference Thermodynamic Integration Augmented with Hamiltonian Replica ExchangeParallelized-over-parts computation of absolute binding free energy with docking and molecular dynamics.Advances in all atom sampling methods for modeling protein-ligand binding affinitiesSymmetry numbers for rigid, flexible, and fluxional molecules: theory and applicationsImproved Binding Free Energy Predictions from Single-Reference Thermodynamic Integration Augmented with Hamiltonian Replica ExchangeForce Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion Coefficient, and Dielectric Constant.How to deal with multiple binding poses in alchemical relative protein-ligand binding free energy calculations.Phosphorylation Regulates the Bound Structure of an Intrinsically Disordered Protein: The p53-TAZ2 Case.Modeling Protein-Ligand Binding by Mining Minima.Role of Ligand Reorganization and Conformational Restraints on the Binding Free Energies of DAPY Non-Nucleoside Inhibitors to HIV Reverse Transcriptase.Free Energy-Based Virtual Screening and Optimization of RNase H Inhibitors of HIV-1 Reverse Transcriptase.Recent theoretical and computational advances for modeling protein-ligand binding affinitiesAccurate calculation of the absolute free energy of binding for drug molecules.Parmbsc1: a refined force field for DNA simulations.CHARMM-GUI Ligand Binder for absolute binding free energy calculations and its application
P2860
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P2860
On the use of orientational restraints and symmetry corrections in alchemical free energy calculations
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2006 nî lūn-bûn
@nan
2006年の論文
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2006年学术文章
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2006年学术文章
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2006年学术文章
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2006年学术文章
@zh-my
2006年学术文章
@zh-sg
2006年學術文章
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2006年學術文章
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name
On the use of orientational re ...... mical free energy calculations
@en
On the use of orientational re ...... mical free energy calculations
@nl
type
label
On the use of orientational re ...... mical free energy calculations
@en
On the use of orientational re ...... mical free energy calculations
@nl
prefLabel
On the use of orientational re ...... mical free energy calculations
@en
On the use of orientational re ...... mical free energy calculations
@nl
P2860
P356
P1476
On the use of orientational re ...... mical free energy calculations
@en
P2093
Ken A Dill
P2860
P304
P356
10.1063/1.2221683
P407
P577
2006-08-01T00:00:00Z