(Q42377074)

28 October 2017

How wet should be the reaction coordinate for ligand unbinding? (English)

1 reference

28 October 2017

Pratyush Tiwary

1

1 reference

28 October 2017

B J Berne

series ordinal

2

1 reference

28 October 2017

language of work or name

English

0 references

publication date

1 August 2016

1 reference

Journal of Chemical Physics

28 October 2017

1 reference

28 October 2017

145

1 reference

28 October 2017

5

1 reference

28 October 2017

054113

1 reference

Kramers turnover: From energy diffusion to spatial diffusion using metadynamics

28 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4975749

Enhancing Important Fluctuations: Rare Events and Metadynamics from a Conceptual Viewpoint.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4975749

Spectral gap optimization of order parameters for sampling complex molecular systems

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4975749

The drug-target residence time model: a 10-year retrospective

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4975749

GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4975749

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

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4975749

Protein conformational plasticity and complex ligand-binding kinetics explored by atomistic simulations and Markov models

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4975749

Locating landmarks on high-dimensional free energy surfaces

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4975749

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

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4975749

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

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4975749

Optimal Dimensionality Reduction of Multistate Kinetic and Markov-State Models

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4975749

From metadynamics to dynamics.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4975749

How hydrophobic drying forces impact the kinetics of molecular recognition

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4975749

Molecular recognition and ligand association

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4975749

Molecular determinants of drug-receptor binding kinetics

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4975749

Solvent fluctuations in hydrophobic cavity-ligand binding kinetics

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4975749

Mechanism of voltage gating in potassium channels

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4975749

From the Cover: Simplifying the representation of complex free-energy landscapes using sketch-map

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4975749

Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4975749

How does a drug molecule find its target binding site?

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4975749

Fluctuations of water near extended hydrophobic and hydrophilic surfaces

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4975749

Progress and challenges in the automated construction of Markov state models for full protein systems

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4975749

Canonical sampling through velocity rescaling

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4975749

Drug-target residence time and its implications for lead optimization

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4975749

Geometric diffusions as a tool for harmonic analysis and structure definition of data: diffusion maps.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4975749

Reaction coordinates and rates from transition paths

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4975749

Adaptive Multilevel Splitting Method for Molecular Dynamics Calculation of Benzamidine-Trypsin Dissociation Time

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4975749

Solvent Fluctuations Induce Non-Markovian Kinetics in Hydrophobic Pocket-Ligand Binding.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4975749

A time-independent free energy estimator for metadynamics.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4975749

Identification of slow molecular order parameters for Markov model construction

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4975749

Determination of reaction coordinates via locally scaled diffusion map.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4975749

Obtaining reaction coordinates by likelihood maximization.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4975749

Automatic method for identifying reaction coordinates in complex systems.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4975749

Observation of a dewetting transition in the collapse of the melittin tetramer

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4975749

Comparison of simple potential functions for simulating liquid water

16 August 2018

1 reference

Molecular dynamics with coupling to an external bath

21 January 2018

1 reference

Cavity Expulsion and Weak Dewetting of Hydrophobic Solutes in Water

21 January 2018

1 reference

The role of water in host-guest interaction

21 January 2018

1 reference

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

21 January 2018

1 reference

Are Hydrodynamic Interactions Important in the Kinetics of Hydrophobic Collapse?

21 January 2018

1 reference

Assessing the Reliability of the Dynamics Reconstructed from Metadynamics

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/27497545

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Inferring Transition Rates of Networks from Populations in Continuous-Time Markov Processes

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/27497545

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1063/1.4959969

1 reference

28 October 2017

1 reference

0 references

1 reference

28 October 2017

PubMed publication ID

27497545

1 reference