Convergence and error estimation in free energy calculations using the weighted histogram analysis method
about
Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and DynamicsLarge-scale asynchronous and distributed multidimensional replica exchange molecular simulations and efficiency analysisAsynchronous Replica Exchange Software for Grid and Heterogeneous ComputingConformational Changes in Two Inter-Helical Loops of Mhp1 Membrane Transporter.Standard binding free energies from computer simulations: What is the best strategy?Locally weighted histogram analysis and stochastic solution for large-scale multi-state free energy estimation.Free energetics of rigid body association of ubiquitin binding domains: a biochemical model for binding mediated by hydrophobic interaction.Statistically optimal analysis of state-discretized trajectory data from multiple thermodynamic states.Ion-specific induced fluctuations and free energetics of aqueous protein hydrophobic interfaces: toward connecting to specific-ion behaviors at aqueous liquid-vapor interfaces.Computational Recipe for Efficient Description of Large-Scale Conformational Changes in Biomolecular SystemsAssessing the relative stability of dimer interfaces in g protein-coupled receptors.A general theory of DNA-mediated and other valence-limited colloidal interactions.Spherical monovalent ions at aqueous liquid-vapor interfaces: interfacial stability and induced interface fluctuations.Temperature dependence and energetics of single ions at the aqueous liquid-vapor interface.Liquid-vapor interfacial properties of aqueous solutions of guanidinium and methyl guanidinium chloride: influence of molecular orientation on interface fluctuations.Association of alkanes with the aqueous liquid-vapor interface: a reference system for interpreting hydrophobicity generally through interfacial fluctuations.Conformational dynamics of a ligand-free adenylate kinase.Differential stability of the crystallographic interfaces of mu- and kappa-opioid receptorsCooperative DNA Recognition Modulated by an Interplay between Protein-Protein Interactions and DNA-Mediated Allostery.Theory of binless multi-state free energy estimation with applications to protein-ligand binding.Thermodynamics of Micelle Formation and Membrane Fusion Modulate Antimicrobial Lipopeptide Activity.BayesWHAM: A Bayesian approach for free energy estimation, reweighting, and uncertainty quantification in the weighted histogram analysis method.Theory and simulation of ion conduction in the pentameric GLIC channelPhysical characterization and in silico modeling of inulin polymer conformation during vaccine adjuvant particle formation.Current state of theoretical and experimental studies of the voltage-dependent anion channel (VDAC)Self-Learning Adaptive Umbrella Sampling Method for the Determination of Free Energy Landscapes in Multiple Dimensions.Efficient Determination of Free Energy Landscapes in Multiple Dimensions from Biased Umbrella Sampling Simulations Using Linear Regression.A Stochastic Solution to the Unbinned WHAM Equations.Accelerating the weighted histogram analysis method by direct inversion in the iterative subspace.Multiensemble Markov models of molecular thermodynamics and kinetics.Efficient determination of protein-protein standard binding free energies from first principles.Role of the pH in state-dependent blockade of hERG currents.Molecular lock regulates binding of glycine to a primitive NMDA receptor.Enhanced stochastic fluctuations to measure steep adhesive energy landscapesBoth DNA global deformation and repair enzyme contacts mediate flipping of thymine dimer damage.Computational Membrane Biophysics: From Ion Channels Interactions with Drugs to Cellular Function.Molecular dynamics-based strength estimates of beta solenoid proteins.Eigenvector method for umbrella sampling enables error analysisGlobal deformation facilitates flipping of damaged 8-oxo-guanine and guanine in DNA.Free energy analysis and mechanism of base pair stacking in nicked DNA.
P2860
Q26749162-D9B9E7B8-BC10-446F-8184-D3B36D3933D0Q27334394-FA8703BF-D310-4600-9769-3CF4C4E2CE62Q28834607-EDCB123D-3A9A-41EE-B80D-EF4AB5BA9D8EQ30376837-00E7AF37-8181-425B-875E-FF4D418E00F0Q30540733-68F34268-FC8F-40C7-A0EE-BE24EEFBCC8CQ30702443-284A0240-4D9C-4708-9D76-A5884AD7F2DAQ30733711-F96AC933-F2B2-4395-897F-366E1FCD533FQ30875118-37277897-2918-4D7C-9225-AA5E05379940Q33567103-55FE3C77-35DD-4B43-880A-C154ECE17CE5Q33874106-5255972F-5E51-48A8-B960-FE0BA3AB1C3AQ34295521-B422BB5C-AFE1-402F-AF55-FEA93632CAF1Q34408429-E935FA90-4B1E-4305-A44B-3414FE4789D8Q34411170-A0E6C5D7-06D0-4D67-A76B-931856D51376Q34411176-2BE5C299-030D-4A2F-98DE-D406D0FD8A9AQ34438103-DBCEA034-4FDC-44A0-90B1-E5AF043F3C8CQ34543355-EC680429-6818-4B88-8A51-D60681CD18FBQ34826682-CC648EE7-3445-4BC6-B024-EC779A0743E2Q35126350-A4F43FCE-B424-466D-8CC0-99BF56AE7651Q35661490-E9716CB4-3F3C-4AC8-9996-3ADF2A7AAE7DQ35921319-815E5233-17AA-4B0A-BC7B-7F7D3D4BBBB4Q35990126-3C3370B9-017B-45F6-89F4-B07A47F5C74EQ36364393-C78E76FD-47C1-49DF-8A44-3F3050D6D341Q36600215-E4943EC4-1FCE-4DDB-A988-57E3DDCA75B6Q36805270-B4FDF9DC-D0C9-4054-9FDF-22F32A7E438AQ36927467-A885B12F-485F-47D6-B168-07B89EB54A2CQ36960616-CBA4C8E0-D724-40A4-99A3-1298FA226721Q36972268-4DA47273-3F2B-442B-AAB4-1E19F6F1E130Q36973107-9C5B64C9-C41A-46D6-B36F-A9E59EBD86CDQ37114175-CE1C974F-152D-4D00-AA23-93B62E950252Q37183610-CF4C2B8C-5457-4A43-BEC4-4CA5A73B3400Q37257220-8B05600C-FCB8-42BF-A342-E88564DF3510Q37330268-BCDB377A-8E57-4C61-BF35-44B2B3C42611Q37398026-F3BAE31E-6040-4580-A629-F939D46AEAB5Q37514962-3C2D35C7-BF64-4FB3-858E-C641B6A25443Q37609422-90DB8EB8-8EC9-4863-9A25-DD5145973D1BQ38605343-8C1D9AAF-76F1-4BF2-90FB-7ED8967D4280Q38626335-6E82A9AE-A134-4F41-B554-F79CCAAC5788Q39430187-D89A7317-7141-437E-9F21-AD58D6780E40Q39618043-B45795F9-0813-4F90-81D8-678C7CC5307FQ41005478-B8F26267-23D9-4DE4-8D51-A5F15E119EF9
P2860
Convergence and error estimation in free energy calculations using the weighted histogram analysis method
description
2011 nî lūn-bûn
@nan
2011年の論文
@ja
2011年論文
@yue
2011年論文
@zh-hant
2011年論文
@zh-hk
2011年論文
@zh-mo
2011年論文
@zh-tw
2011年论文
@wuu
2011年论文
@zh
2011年论文
@zh-cn
name
Convergence and error estimati ...... hted histogram analysis method
@ast
Convergence and error estimati ...... hted histogram analysis method
@en
type
label
Convergence and error estimati ...... hted histogram analysis method
@ast
Convergence and error estimati ...... hted histogram analysis method
@en
prefLabel
Convergence and error estimati ...... hted histogram analysis method
@ast
Convergence and error estimati ...... hted histogram analysis method
@en
P2860
P356
P1476
Convergence and error estimati ...... hted histogram analysis method
@en
P2093
Fangqiang Zhu
P2860
P304
P356
10.1002/JCC.21989
P577
2011-11-23T00:00:00Z