(Q36120365)

12 August 2017

Role of water and steric constraints in the kinetics of cavity-ligand unbinding (English)

1 reference

12 August 2017

Pratyush Tiwary

1

1 reference

12 August 2017

Jagannath Mondal

series ordinal

2

1 reference

12 August 2017

Joseph A Morrone

series ordinal

3

1 reference

12 August 2017

B J Berne

series ordinal

4

1 reference

12 August 2017

language of work or name

English

0 references

publication date

14 September 2015

1 reference

Proceedings of the National Academy of Sciences of the United States of America

12 August 2017

1 reference

12 August 2017

112

1 reference

12 August 2017

39

1 reference

12 August 2017

12015-12019

1 reference

Pathways to dewetting in hydrophobic confinement.

12 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4593114

Kinetics of protein-ligand unbinding: Predicting pathways, rates, and rate-limiting steps

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4593114

Role of Desolvation in Thermodynamics and Kinetics of Ligand Binding to a Kinase

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4593114

How hydrophobic drying forces impact the kinetics of molecular recognition

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4593114

Molecular determinants of drug-receptor binding kinetics

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4593114

Solvent fluctuations in hydrophobic cavity-ligand binding kinetics

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4593114

Evaporation rate of water in hydrophobic confinement

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4593114

How does a drug molecule find its target binding site?

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4593114

Water in cavity-ligand recognition

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4593114

Dewetting and hydrophobic interaction in physical and biological systems

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4593114

Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4593114

Water in nonpolar confinement: from nanotubes to proteins and beyond

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4593114

Motifs for molecular recognition exploiting hydrophobic enclosure in protein-ligand binding

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4593114

Drug-target residence time and its implications for lead optimization

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4593114

Reaction coordinates and rates from transition paths

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4593114

Escaping free-energy minima

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4593114

Transition path sampling: throwing ropes over rough mountain passes, in the dark.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4593114

The hydrophobic pocket of cyclophilin is the binding site for the human immunodeficiency virus type 1 Gag polyprotein

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4593114

Just add water! The effect of water on the specificity of protein-ligand binding sites and its potential application to drug design

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4593114

From metadynamics to dynamics.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4593114

A time-independent free energy estimator for metadynamics.

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4593114

Well-tempered metadynamics converges asymptotically.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4593114

Reconstructing the equilibrium Boltzmann distribution from well-tempered metadynamics.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4593114

The role of solvent fluctuations in hydrophobic assembly.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4593114

Effect of pressure on the phase behavior and structure of water confined between nanoscale hydrophobic and hydrophilic plates.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4593114

Reversible multiple time scale molecular dynamics

23 September 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1516652112

PLUMED: A portable plugin for free-energy calculations with molecular dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1516652112

Cavity Expulsion and Weak Dewetting of Hydrophobic Solutes in Water

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1516652112

Interplay between Hydrodynamics and the Free Energy Surface in the Assembly of Nanoscale Hydrophobes

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1516652112

Are Hydrodynamic Interactions Important in the Kinetics of Hydrophobic Collapse?

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1516652112

Assessing the Reliability of the Dynamics Reconstructed from Metadynamics

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26371312

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Predicting slow structural transitions in macromolecular systems: Conformational flooding

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26371312

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1073/PNAS.1516652112

1 reference

12 August 2017

0 references

1 reference

0 references

1 reference

12 August 2017

1 reference