(Q35822656)

10 August 2017

Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning (English)

1 reference

10 August 2017

Lane W Votapka

1

1 reference

PMC publication ID

4624728

10 August 2017

Rommie E Amaro

series ordinal

2

1 reference

10 August 2017

27 October 2015

1 reference

PLOS Computational Biology

10 August 2017

1 reference

10 August 2017

11

1 reference

10 August 2017

10

1 reference

10 August 2017

e1004381

1 reference

Creative Commons Attribution 4.0 International

10 August 2017

start time

27 October 2015

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

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1 reference

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Full kinetics of CO entry, internal diffusion, and exit in myoglobin from transition-path theory simulations

27 July 2018

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Foundations of biomolecular modeling

27 July 2018

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27 July 2018

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Long-timescale molecular dynamics simulations elucidate the dynamics and kinetics of exposure of the hydrophobic patch in troponin C

27 July 2018

1 reference

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BDflex: a method for efficient treatment of molecular flexibility in calculating protein-ligand binding rate constants from brownian dynamics simulations

27 July 2018

1 reference

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Oncogenic mutations counteract intrinsic disorder in the EGFR kinase and promote receptor dimerization

27 July 2018

1 reference

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Calculating kinetics and pathways of protein-ligand association

27 July 2018

1 reference

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How does a drug molecule find its target binding site?

27 July 2018

1 reference

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The moderately efficient enzyme: evolutionary and physicochemical trends shaping enzyme parameters

27 July 2018

1 reference

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Revisiting and computing reaction coordinates with Directional Milestoning

27 July 2018

1 reference

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MDAnalysis: a toolkit for the analysis of molecular dynamics simulations

27 July 2018

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Browndye: A Software Package for Brownian Dynamics

27 July 2018

1 reference

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Milestoning without a Reaction Coordinate

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4624728

Everything you wanted to know about Markov State Models but were afraid to ask

27 July 2018

1 reference

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Atomically detailed simulation of the recovery stroke in myosin by Milestoning

27 July 2018

1 reference

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Very fast prediction and rationalization of pKa values for protein-ligand complexes

27 July 2018

1 reference

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A milestoning study of the kinetics of an allosteric transition: atomically detailed simulations of deoxy Scapharca hemoglobin

27 July 2018

1 reference

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Scalable molecular dynamics with NAMD

27 July 2018

1 reference

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Finite element solution of the steady-state Smoluchowski equation for rate constant calculations

27 July 2018

1 reference

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A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations

27 July 2018

1 reference

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Molecular dynamics simulations of biomolecules

27 July 2018

1 reference

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Electrostatics of nanosystems: application to microtubules and the ribosome

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4624728

Crystallographic structures of bovine copper-zinc superoxide dismutase reveal asymmetry in two subunits: functionally important three and five coordinate copper sites captured in the same crystal

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4624728

The kinetic cycle of cardiac troponin C: calcium binding and dissociation at site II trigger slow conformational rearrangements.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4624728

Calcium-induced structural transition in the regulatory domain of human cardiac troponin C

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4624728

Simulation of the diffusional association of barnase and barstar.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4624728

VMD: visual molecular dynamics

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4624728

Catch bond-like kinetics of helix cracking: network analysis by molecular dynamics and milestoning

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4624728

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

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4624728

Pathway and mechanism of drug binding to G-protein-coupled receptors.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4624728

Markov state models based on milestoning.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4624728

Markov models of molecular kinetics: generation and validation

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4624728

Markovian milestoning with Voronoi tessellations

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4624728

On the assumptions underlying milestoning

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4624728

Probability distributions of molecular observables computed from Markov models.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4624728

Coarse master equations for peptide folding dynamics.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4624728

Hierarchical analysis of conformational dynamics in biomolecules: transition networks of metastable states.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4624728

Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4624728

Extending molecular dynamics time scales with milestoning: example of complex kinetics in a solvated peptide.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4624728

Drug-target residence time and its implications for lead optimization

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4624728

Structural based insights into the role of troponin in cardiac muscle pathophysiology

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4624728

Computing time scales from reaction coordinates by milestoning.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4624728

Designing calcium-sensitizing mutations in the regulatory domain of cardiac troponin C.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4624728

Brownian dynamics simulation of protein-protein diffusional encounter

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4624728

Millisecond-scale molecular dynamics simulations on Anton

24 September 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004381

Semianalytical treatment of solvation for molecular mechanics and dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004381

Comparison of simple potential functions for simulating liquid water

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004381

Molecular Dynamics Simulations of the Enzyme Cu, Zn Superoxide Dismutase

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004381

A simple polarizable model of water based on classical Drude oscillators

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004381

Point charge distributions and electrostatic steering in enzyme/substrate encounter: Brownian dynamics of modified copper/zinc superoxide dismutases

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26505480

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Molecular simulations of diffusion and association in multimacromolecular systems

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26505480

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Electrostatic interactions in the reaction mechanism of bovine erythrocyte superoxide dismutase

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26505480

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PCBI.1004381

1 reference

journals/ploscb/VotapkaA15

10 August 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

PMC publication ID

4624728

10 August 2017

PubMed publication ID

26505480

1 reference

PMC publication ID

4624728