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Evaluating the accuracy of the umbrella sampling plots with different dissociation paths, conformational changes, and structure preparation

https://doi.org/10.1101/169532
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/anie.200502770openalex-snapshot
NMR Characterization of Kinase p38 Dynamics in Free and Ligand‐Bound Forms
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Hybrid Steered Molecular Dynamics‐Docking: An Efficient Solution to the Problem of Ranking Inhibitor Affinities Against a Flexible Drug Target.
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Exploring coumarin egress channels in human cytochrome p450 2a6 by random acceleration and steered molecular dynamics simulations
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Frontiers in free‐energy calculations of biological systems
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Steered molecular dynamics approach for promising drugs for influenza A virus targeting M2 channel proteins
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Monte Carlo free energy estimates using non-Boltzmann sampling: Application to the sub-critical Lennard-Jones fluid
inferredcites →https://doi.org/10.1016/0021-9991(77)90121-8openalex-snapshot
Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling
inferredcites →https://doi.org/10.1016/j.ab.2003.10.025openalex-snapshot
A Biacore biosensor method for detailed kinetic binding analysis of small molecule inhibitors of p38α mitogen-activated protein kinase
inferredcites →https://doi.org/10.1016/j.bbamcr.2007.03.010openalex-snapshot
p38 MAP-Kinases pathway regulation, function and role in human diseases
inferredcites →https://doi.org/10.1016/j.biomaterials.2013.09.061openalex-snapshot
Cyclodextrins in non-viral gene delivery
inferredcites →https://doi.org/10.1016/j.bpc.2016.01.003openalex-snapshot
Steered molecular dynamics study of inhibitor binding in the internal binding site in dehaloperoxidase-hemoglobin
inferredcites →https://doi.org/10.1016/s0010-4655(00)00215-0openalex-snapshot
Extension to the weighted histogram analysis method: combining umbrella sampling with free energy calculations
inferredcites →https://doi.org/10.1016/s0032-9592(03)00258-9openalex-snapshot
Cyclodextrins and their uses: a review
inferredcites →https://doi.org/10.1016/s0079-6468(08)70091-2openalex-snapshot
1 p38 MAP Kinase: Molecular Target for the Inhibition of Pro-inflammatory Cytokines
inferredcites →https://doi.org/10.1016/s0092-8674(02)00741-9openalex-snapshot
The Conformational Plasticity of Protein Kinases
inferredcites →https://doi.org/10.1016/s0734-9750(02)00020-4openalex-snapshot
Biotechnological applications of cyclodextrins
inferredcites →https://doi.org/10.1016/s0969-2126(98)00113-0openalex-snapshot
Structural basis of inhibitor selectivity in MAP kinases
inferredcites →https://doi.org/10.1021/acs.jctc.5b00340openalex-snapshot
Computing Protein–Protein Association Affinity with Hybrid Steered Molecular Dynamics
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Directly Binding Rather than Induced-Fit Dominated Binding Affinity Difference in (S)- and (R)-Crizotinib Bound MTH1
inferredcites →https://doi.org/10.1021/acs.jpcb.6b05125openalex-snapshot
Leveraging the Information from Markov State Models To Improve the Convergence of Umbrella Sampling Simulations
inferredcites →https://doi.org/10.1021/ci500164qopenalex-snapshot
Free Energy Predictions of Ligand Binding to an α-Helix Using Steered Molecular Dynamics and Umbrella Sampling Simulations
inferredcites →https://doi.org/10.1021/ci500527jopenalex-snapshot
Unbinding Pathways of VEGFR2 Inhibitors Revealed by Steered Molecular Dynamics
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Free energy calculations: Applications to chemical and biochemical phenomena
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Thermodynamic and Kinetic Data for Macrocycle Interaction with Cations, Anions, and Neutral Molecules
inferredcites →https://doi.org/10.1021/cr4005988openalex-snapshot
Collective Variable Approaches for Single Molecule Flexible Fitting and Enhanced Sampling
inferredcites →https://doi.org/10.1021/cr970011jopenalex-snapshot
Biomimetic Reactions Catalyzed by Cyclodextrins and Their Derivatives
inferredcites →https://doi.org/10.1021/cr970015oopenalex-snapshot
Complexation Thermodynamics of Cyclodextrins
inferredcites →https://doi.org/10.1021/cr970019topenalex-snapshot
NMR Studies of Cyclodextrins and Cyclodextrin Complexes
inferredcites →https://doi.org/10.1021/cs200171uopenalex-snapshot
Biomimetic Catalysis
inferredcites →https://doi.org/10.1021/ct2003786openalex-snapshot
Improved Binding Free Energy Predictions from Single-Reference Thermodynamic Integration Augmented with Hamiltonian Replica Exchange
inferredcites →https://doi.org/10.1021/ct2006902openalex-snapshot
Force and Stress along Simulated Dissociation Pathways of Cucurbituril–Guest Systems
inferredcites →https://doi.org/10.1021/ct300348wopenalex-snapshot
Local Sampling in Steered Monte Carlo Simulations Decreases Dissipation and Enhances Free Energy Estimates via Nonequilibrium Work Theorems
inferredcites →https://doi.org/10.1021/ct3008099openalex-snapshot
Standard Binding Free Energies from Computer Simulations: What Is the Best Strategy?
inferredcites →https://doi.org/10.1021/ct8002354openalex-snapshot
Standard Free Energy of Binding from a One-Dimensional Potential of Mean Force
inferredcites →https://doi.org/10.1021/ja00172a038openalex-snapshot
Semianalytical treatment of solvation for molecular mechanics and dynamics
inferredcites →https://doi.org/10.1021/ja902010popenalex-snapshot
Development of a Fluorescent-Tagged Kinase Assay System for the Detection and Characterization of Allosteric Kinase Inhibitors
inferredcites →https://doi.org/10.1021/jp010535uopenalex-snapshot
Molecular Recognition Kinetics of β-Cyclodextrin for Several Alcohols by Ultrasonic Relaxation Method
inferredcites →https://doi.org/10.1021/jp058205nopenalex-snapshot
Dynamic Study of Interaction between β-Cyclodextrin and Aspirin by the Ultrasonic Relaxation Method
inferredcites →https://doi.org/10.1021/jp212168fopenalex-snapshot
Calculation of Partition Functions and Free Energies of a Binary Mixture Using the Energy Partitioning Method: Application to Carbon Dioxide and Methane
inferredcites →https://doi.org/10.1021/jp504942topenalex-snapshot
Implementation of the Forward–Reverse Method for Calculating the Potential of Mean Force Using a Dynamic Restraining Protocol
inferredcites →https://doi.org/10.1021/jp802963xopenalex-snapshot
Thermodynamic and Kinetic Characterization of Host−Guest Association between Bolaform Surfactants and α- and β-Cyclodextrins
inferredcites →https://doi.org/10.1021/jp9803844openalex-snapshot
Complexation of Naphthylethanols with β-Cyclodextrin
inferredcites →https://doi.org/10.1021/jp9833909openalex-snapshot
Kinetics of Inclusion Reactions of β-Cyclodextrin with Several Dihydroxycholate Ions Studied by NMR Spectroscopy
inferredcites →https://doi.org/10.1023/b:jcam.0000035186.90683.f2openalex-snapshot
VEGA – An open platform to develop chemo-bio-informatics applications, using plug-in architecture and script programming
inferredcites →https://doi.org/10.1038/nrd1177openalex-snapshot
p38 MAP kinases: key signalling molecules as therapeutic targets for inflammatory diseases
inferredcites →https://doi.org/10.1038/nrd1576openalex-snapshot
Cyclodextrin-based pharmaceutics: past, present and future
inferredcites →https://doi.org/10.1038/nrd2796openalex-snapshot
The influence of lead discovery strategies on the properties of drug candidates
inferredcites →https://doi.org/10.1038/srep08457openalex-snapshot
Revealing the favorable dissociation pathway of type II kinase inhibitors via enhanced sampling simulations and two-end-state calculations
inferredcites →https://doi.org/10.1039/c1cp20854copenalex-snapshot
Molecular dynamics studies of native and substituted cyclodextrins in different media: 1. Charge derivation and force field performances
inferredcites →https://doi.org/10.1063/1.1740409openalex-snapshot
High-Temperature Equation of State by a Perturbation Method. I. Nonpolar Gases
inferredcites →https://doi.org/10.1063/1.1755656openalex-snapshot
Accelerated molecular dynamics: A promising and efficient simulation method for biomolecules
inferredcites →https://doi.org/10.1063/1.445869openalex-snapshot
Comparison of simple potential functions for simulating liquid water
inferredcites →https://doi.org/10.1073/pnas.0409005102openalex-snapshot
Calculation of absolute protein–ligand binding free energy from computer simulations
inferredcites →https://doi.org/10.1073/pnas.102649299openalex-snapshot
Energetics of glycerol conduction through aquaglyceroporin GlpF
inferredcites →https://doi.org/10.1146/annurev.bb.18.060189.002243openalex-snapshot
Free Energy Via Molecular Simulation: Applications to Chemical and Biomolecular Systems
inferredcites →https://doi.org/10.1177/154405910708600902openalex-snapshot
p38 Pathway Kinases as Anti-inflammatory Drug Targets
inferredcites →https://doi.org/10.1208/pt060243openalex-snapshot
Cyclodextrins in drug delivery: An updated review
inferredcites →https://doi.org/10.1371/journal.pcbi.1003729openalex-snapshot
P-loop Conformation Governed Crizotinib Resistance in G2032R-Mutated ROS1 Tyrosine Kinase: Clues from Free Energy Landscape
inferredcites →https://doi.org/10.1371/journal.pone.0008470openalex-snapshot
Steered Molecular Dynamics Simulations Reveal the Likelier Dissociation Pathway of Imatinib from Its Targeting Kinases c-Kit and Abl
inferredcites →https://doi.org/10.2174/092986706779026165openalex-snapshot
Towards Predictive Ligand Design With Free-Energy Based Computational Methods?
inferredcites →https://doi.org/10.2174/156802606775270323openalex-snapshot
New Approaches to the Treatment of Inflammatory Disorders Small Molecule inhibitors of p38 MAP Kinase

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1007/978-981-15-8936-2_7openalex-snapshot
Predicting Protein Folding and Protein Stability by Molecular Dynamics Simulations for Computational Drug Discovery
inferred← citeshttps://doi.org/10.2174/1389200223666220315160835openalex-snapshot
Classical and Machine Learning Methods for Protein - Ligand Binding Free Energy Estimation
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