Advances in all atom sampling methods for modeling protein-ligand binding affinities
about
Exploring the role of receptor flexibility in structure-based drug discoveryLarge-scale asynchronous and distributed multidimensional replica exchange molecular simulations and efficiency analysisAsynchronous Replica Exchange Software for Grid and Heterogeneous ComputingFree Energy Perturbation Calculation of Relative Binding Free Energy between Broadly Neutralizing Antibodies and the gp120 Glycoprotein of HIV-1.Perspective: Alchemical free energy calculations for drug discovery.Alchemical free energy methods for drug discovery: progress and challengesRelative Binding Enthalpies from Molecular Dynamics Simulations Using a Direct Method.Entropy-enthalpy compensation: role and ramifications in biomolecular ligand recognition and design.Large scale affinity calculations of cyclodextrin host-guest complexes: Understanding the role of reorganization in the molecular recognition process.Virtual screening of integrase inhibitors by large scale binding free energy calculations: the SAMPL4 challenge.Ligand binding and dynamics of the monomeric epidermal growth factor receptor ectodomain.Improved Binding Free Energy Predictions from Single-Reference Thermodynamic Integration Augmented with Hamiltonian Replica ExchangeMulti-Site λ-dynamics for simulated Structure-Activity Relationship studiesOn achieving high accuracy and reliability in the calculation of relative protein-ligand binding affinities.Conformational Transitions and Convergence of Absolute Binding Free Energy Calculations.Locating binding poses in protein-ligand systems using reconnaissance metadynamics.Theory of binless multi-state free energy estimation with applications to protein-ligand binding.Binding Energy Distribution Analysis Method: Hamiltonian Replica Exchange with Torsional Flattening for Binding Mode Prediction and Binding Free Energy EstimationRole of Ligand Reorganization and Conformational Restraints on the Binding Free Energies of DAPY Non-Nucleoside Inhibitors to HIV Reverse Transcriptase.Prediction of SAMPL3 host-guest affinities with the binding energy distribution analysis method (BEDAM).Free Energy-Based Virtual Screening and Optimization of RNase H Inhibitors of HIV-1 Reverse Transcriptase.Exploration of gated ligand binding recognizes an allosteric site for blocking FABP4-protein interaction.Characterization of the three-dimensional free energy manifold for the uracil ribonucleoside from asynchronous replica exchange simulations.(Ala)(4)-X-(Ala)4 as a model system for the optimization of the χ1 and χ2 amino acid side-chain dihedral empirical force field parametersA New Maximum Likelihood Approach for Free Energy Profile Construction from Molecular Simulations.BEDAM binding free energy predictions for the SAMPL4 octa-acid host challenge.Efficient determination of protein-protein standard binding free energies from first principles.Roadmaps through free energy landscapes calculated using the multi-dimensional vFEP approach.Sampling of conformational ensemble for virtual screening using molecular dynamics simulations and normal mode analysis.Multiple binding modes of ibuprofen in human serum albumin identified by absolute binding free energy calculations.A unique binding mode of the eukaryotic translation initiation factor 4E for guiding the design of novel peptide inhibitors.Sensitivity in Binding Free Energies Due to Protein ReorganizationThe Movable Type Method Applied to Protein-Ligand BindingDistinguishing binders from false positives by free energy calculations: fragment screening against the flap site of HIV proteaseCurrent and emerging opportunities for molecular simulations in structure-based drug design.Bennett's acceptance ratio and histogram analysis methods enhanced by umbrella sampling along a reaction coordinate in configurational space.Resolving the Ligand-Binding Specificity in c-MYC G-Quadruplex DNA: Absolute Binding Free Energy Calculations and SPR Experiment.In Silico prediction of the molecular basis of ClTx and AaCTx interaction with matrix metalloproteinase-2 (MMP-2) to inhibit glioma cell invasion.Toward Fast and Accurate Binding Affinity Prediction with pmemdGTI: An Efficient Implementation of GPU-Accelerated Thermodynamic Integration.I. Dissociation free energies of drug-receptor systems via non-equilibrium alchemical simulations: a theoretical framework.
P2860
Q27001129-9FD906BE-5873-4002-A880-9290B46AF8B4Q27334394-85434B8F-B270-46C5-81A7-EAA71D2A0B09Q28834607-196C1425-14D2-41A8-ACE6-A2AF9F68F569Q30395868-D1F94562-90E3-4DEA-9FE1-FD67FFA68273Q30422862-DEAF8283-B116-40F6-8FC5-7E2AB5E0BE15Q30427576-E2B1C5E9-9F1D-4B85-AA4B-99B9574B7D2FQ33893521-E3DA397C-BD45-4B25-981B-32BD73CC118EQ34011410-D5FF26FA-A95D-436D-9A72-EFB1296D9107Q34065083-3B4F6BE1-63D6-45EA-BD93-8945DCBA9BCDQ34065423-95ACF2F7-C492-460A-88C7-4F7D8DD250F8Q34805228-A0611FF1-0905-46FB-91AF-994978691180Q35435838-9FF683EF-893C-467E-B1F8-2EF74444CDCBQ35572848-C0518A68-0988-43C5-B5D3-CC66682647BAQ35751099-E20895DE-5FFA-4E14-BBE3-78298F204A3CQ35773629-6CC8E75C-553E-4DD1-B78C-CD18222A91BFQ35887173-972DC5B5-CD73-452C-9AFF-FFF6D1B3A278Q35921319-8DBA2539-C77A-4E90-A26A-78FD3BC49D03Q35987280-2DC5C23F-396C-44AA-8D30-C8F5F5F7A896Q36029898-E815E845-2E03-4C4F-928D-CA1193204E43Q36060565-D18F3B36-3883-4BDD-A104-B967D6485208Q36155983-166A7E68-82CA-453A-8E05-C49799B55B50Q36342813-E1F8793A-2152-402B-BAA4-C7EB37C8A46EQ36556919-1B5ADA01-DC03-43FF-8D0B-0AC279A3BE69Q36605195-001CA912-FCB4-471D-8345-D074B16CD94AQ36634357-87C7F73F-AF9E-4BDD-B84B-7D7BBDB0A540Q36801376-981305D1-1C6D-47BB-ACAB-E120A36FDF42Q37257220-F75B134A-1896-4B46-BC71-50B890EAA603Q37549538-A0A3F0F0-C9E3-4DDB-BFE0-B8F84B681137Q38939477-6C6E4BBC-3A22-46EF-A23D-223A5C9AA80CQ39181234-291586C1-6367-41AE-8383-9277EB05FEBCQ40900248-E758EF1A-A376-4F40-A3D8-33CE3A276D00Q41081254-2C628A64-7792-4F72-9FD2-EEE974DE703BQ41852852-EBABB994-3792-4210-8F7F-716B7EBCFA65Q41989179-B7248537-6A79-4912-A686-E9FF81000CABQ43056042-9CDDB845-AF8D-4EE1-A483-B44926CDBA6AQ44758321-0BE7DE53-C18A-40B5-A43A-C0F641082024Q46096236-C9FA8D9B-82C2-4327-BE45-88B43491035EQ46231247-20A523E9-CCE4-46C5-B2EF-E51755520E83Q48271066-1E804B4E-5215-4F13-86C1-6B77D71889E1Q50643424-9940FE19-5DA2-437B-84AC-9F1736FE69CE
P2860
Advances in all atom sampling methods for modeling protein-ligand binding affinities
description
2011 nî lūn-bûn
@nan
2011 թուականի Փետրուարին հրատարակուած գիտական յօդուած
@hyw
2011 թվականի փետրվարին հրատարակված գիտական հոդված
@hy
2011年の論文
@ja
2011年学术文章
@wuu
2011年学术文章
@zh-cn
2011年学术文章
@zh-hans
2011年学术文章
@zh-my
2011年学术文章
@zh-sg
2011年學術文章
@yue
name
Advances in all atom sampling methods for modeling protein-ligand binding affinities
@ast
Advances in all atom sampling methods for modeling protein-ligand binding affinities
@en
Advances in all atom sampling methods for modeling protein-ligand binding affinities
@nl
type
label
Advances in all atom sampling methods for modeling protein-ligand binding affinities
@ast
Advances in all atom sampling methods for modeling protein-ligand binding affinities
@en
Advances in all atom sampling methods for modeling protein-ligand binding affinities
@nl
prefLabel
Advances in all atom sampling methods for modeling protein-ligand binding affinities
@ast
Advances in all atom sampling methods for modeling protein-ligand binding affinities
@en
Advances in all atom sampling methods for modeling protein-ligand binding affinities
@nl
P2860
P1476
Advances in all atom sampling methods for modeling protein-ligand binding affinities
@en
P2093
Emilio Gallicchio
Ronald M Levy
P2860
P304
P356
10.1016/J.SBI.2011.01.010
P577
2011-02-19T00:00:00Z