(Q37614213)

21 August 2017

Simulation-Based Approaches for Determining Membrane Permeability of Small Compounds (English)

1 reference

21 August 2017

Christopher T Lee

1

0 references

Christopher N Rowley

object named as

Christopher N Rowley

8

0 references

James C Gumbart

12

object named as

James C Gumbart

1 reference

21 August 2017

Jeffrey Comer

2

1 reference

21 August 2017

Conner Herndon

3

1 reference

21 August 2017

Nelson Leung

4

1 reference

21 August 2017

Anna Pavlova

5

1 reference

21 August 2017

Robert V Swift

6

1 reference

21 August 2017

Chris Tung

7

1 reference

21 August 2017

Rommie E Amaro

9

1 reference

21 August 2017

Christophe Chipot

10

1 reference

21 August 2017

Yi Wang

11

1 reference

21 August 2017

4 April 2016

1 reference

Journal of Chemical Information and Modeling

21 August 2017

1 reference

21 August 2017

56

1 reference

21 August 2017

4

1 reference

21 August 2017

721-733

1 reference

Accurate and reliable prediction of relative ligand binding potency in prospective drug discovery by way of a modern free-energy calculation protocol and force field

21 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5280572

CHARMM-GUI Membrane Builder toward realistic biological membrane simulations

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5280572

Modeling kinetics and equilibrium of membranes with fields: milestoning analysis and implication to permeation

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5280572

A method to predict blood-brain barrier permeability of drug-like compounds using molecular dynamics simulations

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5280572

Indolicidin binding induces thinning of a lipid bilayer

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5280572

Free energetics of arginine permeation into model DMPC lipid bilayers: coupling of effective counterion concentration and lateral bilayer dimensions

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5280572

A polarizable force field of dipalmitoylphosphatidylcholine based on the classical Drude model for molecular dynamics simulations of lipids

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5280572

Systematic improvement of a classical molecular model of water

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5280572

Back to the future: can physical models of passive membrane permeability help reduce drug candidate attrition and move us beyond QSPR?

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5280572

A Bayesian inference scheme to extract diffusivity and potential fields from confined single-molecule trajectories

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5280572

Theory of binless multi-state free energy estimation with applications to protein-ligand binding

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5280572

Unassisted transport of N-acetyl-L-tryptophanamide through membrane: experiment and simulation of kinetics

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5280572

Water Permeation Through DMPC Lipid Bilayers using Polarizable Charge Equilibration Force Fields.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5280572

Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5280572

CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5280572

ADDME--Avoiding Drug Development Mistakes Early: central nervous system drug discovery perspective

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5280572

Distribution of amino acids in a lipid bilayer from computer simulations.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5280572

Position-resolved free energy of solvation for amino acids in lipid membranes from molecular dynamics simulations.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5280572

Single-molecule experiments in vitro and in silico

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5280572

On the thermodynamic stability of a charged arginine side chain in a transmembrane helix

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5280572

Liposomal drug transport: a molecular perspective from molecular dynamics simulations in lipid bilayers

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5280572

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5280572

Caco-2 cell permeability assays to measure drug absorption.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5280572

Interfacial free energy and the hydrophobic effect

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5280572

Scalable molecular dynamics with NAMD

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5280572

Can the pharmaceutical industry reduce attrition rates?

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5280572

Permeation across hydrated DPPC lipid bilayers: simulation of the titrable amphiphilic drug valproic acid

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5280572

In silico ADME/Tox: why models fail

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5280572

Escaping free-energy minima

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5280572

Efficient, Multiple-Range Random Walk Algorithm to Calculate the Density of States

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5280572

Caco-2 monolayers in experimental and theoretical predictions of drug transport

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5280572

Molecular dynamics study of unbinding of the avidin-biotin complex

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5280572

The nonelectrolyte permeability of planar lipid bilayer membranes

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5280572

Statistical Convergence of Equilibrium Properties in Simulations of Molecular Solutes Embedded in Lipid Bilayers.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5280572

The great descriptor melting pot: mixing descriptors for the common good of QSAR models

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5280572

Passive Membrane Permeability: Beyond the Standard Solubility-Diffusion Model.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5280572

Calculating Position-Dependent Diffusivity in Biased Molecular Dynamics Simulations

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5280572

Benchmarking of Force Fields for Molecule-Membrane Interactions

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5280572

Accelerating Convergence in Molecular Dynamics Simulations of Solutes in Lipid Membranes by Conducting a Random Walk along the Bilayer Normal

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5280572

Exploring Multidimensional Free Energy Landscapes Using Time-Dependent Biases on Collective Variables.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5280572

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5280572

Automation of the CHARMM General Force Field (CGenFF) I: bond perception and atom typing.

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5280572

Automation of the CHARMM General Force Field (CGenFF) II: assignment of bonded parameters and partial atomic charges.

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5280572

Convergence of Free Energy Profile of Coumarin in Lipid Bilayer

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5280572

Revisiting and computing reaction coordinates with Directional Milestoning

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5280572

Milestoning without a Reaction Coordinate

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5280572

Permeability and electrical properties of thin lipid membranes

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5280572

Partitioning of amino acid side chains into lipid bilayers: results from computer simulations and comparison to experiment

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5280572

Interpretation of nonelectrolyte partition coefficients between dimyristoyl lecithin and water.

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5280572

Use of the Weighted Histogram Analysis Method for the Analysis of Simulated and Parallel Tempering Simulations

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5280572

Diffusive Models of Membrane Permeation with Explicit Orientational Freedom.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5280572

Multiple-Replica Strategies for Free-Energy Calculations in NAMD: Multiple-Walker Adaptive Biasing Force and Walker Selection Rules.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5280572

Calculation of Lipid-Bilayer Permeabilities Using an Average Force.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5280572

Calculating the free energy of transfer of small solutes into a model lipid membrane: Comparison between metadynamics and umbrella sampling.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5280572

Dynamic properties of force fields.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5280572

Calculating diffusion and permeability coefficients with the oscillating forward-reverse method.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5280572

Transfer of arginine into lipid bilayers is nonadditive.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5280572

Permeation of nucleosides through lipid bilayers

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5280572

On the assumptions underlying milestoning

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5280572

Adaptive biasing force method for scalar and vector free energy calculations

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5280572

Diffusion constant of K+ inside Gramicidin A: a comparative study of four computational methods.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5280572

Behaviour of small solutes and large drugs in a lipid bilayer from computer simulations

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5280572

Assessing the efficiency of free energy calculation methods

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5280572

Mechanism of unassisted ion transport across membrane bilayers

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5280572

Membrane-interaction QSAR analysis: application to the estimation of eye irritation by organic compounds.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5280572

Replica Monte Carlo simulation of spin glasses.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5280572

A Novel Approach to the Investigation of Passive Molecular Permeation through Lipid Bilayers from Atomistic Simulations

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5280572

Functional group dependence of solute partitioning to various locations within a DOPC bilayer: a comparison of molecular dynamics simulations with experiment

3 December 2018

1 reference

12 December 2020

Monocarboxylic acid permeation through lipid bilayer membranes

1 reference

12 December 2020

Effects of Cholesterol on the Thermodynamics and Kinetics of Passive Transport of Water through Lipid Membranes

1 reference

12 December 2020

Non-electrolyte permeability across thin lipid membranes

1 reference

12 December 2020

Advantages of a Lowe-Andersen thermostat in molecular dynamics simulations

1 reference

12 December 2020

Why Can Hydrogen Sulfide Permeate Cell Membranes?

1 reference

12 December 2020

Physicochemical high throughput screening: parallel artificial membrane permeation assay in the description of passive absorption processes

1 reference

12 December 2020

Identifiers

DOI

10.1021/ACS.JCIM.6B00022

1 reference

journals/jcisd/LeeCHLPSTRACWG16

21 August 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

21 August 2017

PubMed publication ID

27043429

1 reference