Absolute FKBP binding affinities obtained via nonequilibrium unbinding simulations (Q42729386)

5 November 2017

Absolute FKBP binding affinities obtained via nonequilibrium unbinding simulations (English)

1 reference

5 November 2017

F Marty Ytreberg

1

1 reference

PMCID

2905451

5 November 2017

language of work or name

English

0 references

publication date

1 April 2009

1 reference

Journal of Chemical Physics

5 November 2017

1 reference

5 November 2017

130

1 reference

5 November 2017

16

1 reference

5 November 2017

164906

1 reference

The Confine-and-Release Method: Obtaining Correct Binding Free Energies in the Presence of Protein Conformational Change

5 November 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905451

Ligand escape pathways and (un)binding free energy calculations for the hexameric insulin-phenol complex

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905451

Comparison of free energy methods for molecular systems

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905451

Ligand-release pathways in the pheromone-binding protein of Bombyx mori

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905451

On the use of orientational restraints and symmetry corrections in alchemical free energy calculations

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905451

Parallelized-over-parts computation of absolute binding free energy with docking and molecular dynamics

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905451

Absolute binding free energy calculations using molecular dynamics simulations with restraining potentials

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905451

Potentials of mean force for acetylcholine unbinding from the alpha7 nicotinic acetylcholine receptor ligand-binding domain

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905451

Calculation of absolute protein-ligand binding affinity using path and endpoint approaches

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905451

GROMACS: fast, flexible, and free

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905451

Direct calculation of the binding free energies of FKBP ligands

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905451

Free energy surfaces from single-molecule force spectroscopy

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905451

Calculation of absolute protein-ligand binding free energy from computer simulations

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905451

Comparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamic integration

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905451

Calculation of cyclodextrin binding affinities: energy, entropy, and implications for drug design

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905451

PRODRG: a tool for high-throughput crystallography of protein-ligand complexes

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905451

Calculating potentials of mean force from steered molecular dynamics simulations

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905451

Revisiting free energy calculations: a theoretical connection to MM/PBSA and direct calculation of the association free energy

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905451

Bias and error in estimates of equilibrium free-energy differences from nonequilibrium measurements

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905451

Free energy reconstruction from nonequilibrium single-molecule pulling experiments

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905451

X-ray structures of small ligand-FKBP complexes provide an estimate for hydrophobic interaction energies

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905451

27 May 2018

The Protein Data Bank

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905451

The statistical-thermodynamic basis for computation of binding affinities: a critical review

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905451

Calculation of Standard Binding Free Energies: Aromatic Molecules in the T4 Lysozyme L99A Mutant.

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905451

Calculation of absolute ligand binding free energy to a ribosome-targeting protein as a function of solvent model

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905451

Protein-protein interaction investigated by steered molecular dynamics: the TCR-pMHC complex

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905451

Springs and speeds in free energy reconstruction from irreversible single-molecule pulling experiments

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905451

Using overlap and funnel sampling to obtain accurate free energies from nonequilibrium work measurements

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905451

Improving the efficiency and reliability of free energy perturbation calculations using overlap sampling methods

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905451

Single-step perturbations to calculate free energy differences from unphysical reference states: limits on size, flexibility, and character

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905451

Theory of a systematic computational error in free energy differences.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905451

THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method

16 August 2018

1 reference

Nonequilibrium Equality for Free Energy Differences

21 January 2018

1 reference

Equilibrium free-energy differences from nonequilibrium measurements: A master-equation approach

21 January 2018

1 reference

High‐Temperature Equation of State by a Perturbation Method. I. Nonpolar Gases

21 January 2018

1 reference

Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems

21 January 2018

1 reference

Electrostatic free energy calculations using the generalized solvent boundary potential method

21 January 2018

1 reference

Free energy calculation from steered molecular dynamics simulations using Jarzynski’s equality

21 January 2018

1 reference

Computational Alchemy To Calculate Absolute Protein−Ligand Binding Free Energy

21 January 2018

1 reference

Molecular dynamics with coupling to an external bath

21 January 2018

1 reference

Simulations of the Estrogen Receptor Ligand-Binding Domain: Affinity of Natural Ligands and Xenoestrogens

21 January 2018

1 reference

Fast-growth thermodynamic integration: Error and efficiency analysis

21 January 2018

1 reference

Calculating zeros: Non-equilibrium free energy calculations

21 January 2018

1 reference

Equilibrium Free Energies from Nonequilibrium Measurements Using Maximum-Likelihood Methods

21 January 2018

1 reference

12 December 2020

Evaluating the molecular mechanics poisson-boltzmann surface area free energy method using a congeneric series of ligands to p38 MAP kinase

1 reference

12 December 2020

Potential of mean force calculations of ligand binding to ion channels from Jarzynski's equality and umbrella sampling

1 reference

12 December 2020

Calculation of the relative change in binding free energy of a protein-inhibitor complex

1 reference

12 December 2020

Optimized free energies from bidirectional single-molecule force spectroscopy

1 reference

12 December 2020

A comparison of methods to compute the potential of mean force

1 reference

12 December 2020

Absolute and relative entropies from computer simulation with applications to ligand binding

1 reference

12 December 2020

Identifiers

DOI

10.1063/1.3119261

1 reference

5 November 2017

1 reference

1 reference

5 November 2017

1 reference

PMCID

2905451