(Q35062738)

6 August 2017

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

1 reference

6 August 2017

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25605901%20AND%20SRC:MED&resulttype=core&format=json

31 May 2020

Matteo Salvalaglio

series ordinal

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25605901%20AND%20SRC:MED&resulttype=core&format=json

31 May 2020

4

Michele Parrinello

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25605901%20AND%20SRC:MED&resulttype=core&format=json

31 May 2020

author name string

Pratyush Tiwary

series ordinal

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25605901%20AND%20SRC:MED&resulttype=core&format=json

31 May 2020

language of work or name

English

0 references

publication date

20 January 2015

1 reference

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

6 August 2017

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25605901%20AND%20SRC:MED&resulttype=core&format=json

31 May 2020

volume

112

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25605901%20AND%20SRC:MED&resulttype=core&format=json

31 May 2020

issue

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25605901%20AND%20SRC:MED&resulttype=core&format=json

31 May 2020

page(s)

E386-91

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25605901%20AND%20SRC:MED&resulttype=core&format=json

From metadynamics to dynamics.

31 May 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4321287

Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4321287

Chemical kinetics and mechanisms of complex systems: a perspective on recent theoretical advances

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4321287

Funnel metadynamics as accurate binding free-energy method

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4321287

Molecular determinants of drug-receptor binding kinetics

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4321287

Discrete kinetic models from funneled energy landscape simulations

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4321287

Equilibrium fluctuations of a single folded protein reveal a multitude of potential cryptic allosteric sites

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4321287

Using sketch-map coordinates to analyze and bias molecular dynamics simulations

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4321287

Sampling protein motion and solvent effect during ligand binding

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4321287

Target-drug interactions: first principles and their application to drug discovery

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4321287

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4321287

Improved side-chain torsion potentials for the Amber ff99SB protein force field

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4321287

Molecular basis of cyclooxygenase enzymes (COXs) selective inhibition

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4321287

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4321287

Reactive flux and folding pathways in network models of coarse-grained protein dynamics

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4321287

Random walk in orthogonal space to achieve efficient free-energy simulation of complex systems

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4321287

Calculation of protein-ligand binding free energy by using a polarizable potential

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4321287

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4321287

Canonical sampling through velocity rescaling

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4321287

Calculation of protein-ligand binding affinities.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4321287

Drug-target residence time and its implications for lead optimization

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4321287

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4321287

Flexible docking in solution using metadynamics

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4321287

Escaping free-energy minima

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4321287

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4321287

Long time dynamics of Met-enkephalin: comparison of explicit and implicit solvent models

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4321287

Reaction coordinates of biomolecular isomerization

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4321287

Local elevation: a method for improving the searching properties of molecular dynamics simulation.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4321287

Well-tempered metadynamics converges asymptotically.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4321287

Nudged-elastic band used to find reaction coordinates based on the free energy.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4321287

Investigating the mechanism of substrate uptake and release in the glutamate transporter homologue Glt(Ph) through metadynamics simulations

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4321287

Shielded hydrogen bonds as structural determinants of binding kinetics: application in drug design

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4321287

Determination of reaction coordinates via locally scaled diffusion map.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4321287

Pitfalls of choosing an order parameter for rare event calculations.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4321287

Reconstructing the equilibrium Boltzmann distribution from well-tempered metadynamics.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4321287

The unfolded ensemble and folding mechanism of the C-terminal GB1 beta-hairpin.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4321287

From A to B in free energy space.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4321287

Illustration of transition path theory on a collection of simple examples.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4321287

Global optimization by energy landscape paving.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4321287

Predicting slow structural transitions in macromolecular systems: Conformational flooding

27 September 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1424461112

Mechanistic insight into ligand binding to G-quadruplex DNA

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1424461112

A time-independent free energy estimator for metadynamics.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1424461112

DNA denaturation bubbles: free-energy landscape and nucleation/closure rates.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1424461112

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1424461112

Variational Transition State Theory

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1424461112

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1424461112

The use of proflavin as an indicator in temperature-jump studies of the binding of a competitive inhibitor to trypsin

21 January 2018

1 reference

12 December 2020

Multiple state transition interface sampling of alanine dipeptide in explicit solvent

1 reference

12 December 2020

Assessing the Reliability of the Dynamics Reconstructed from Metadynamics

1 reference

12 December 2020

Variational approach to enhanced sampling and free energy calculations

1 reference

12 December 2020

Identifiers

DOI

10.1073/PNAS.1424461112

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25605901%20AND%20SRC:MED&resulttype=core&format=json

31 May 2020

0 references

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25605901%20AND%20SRC:MED&resulttype=core&format=json

31 May 2020

1 reference