(Q40776037)

23 September 2017

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

1 reference

23 September 2017

1 reference

Nuria Plattner

1

1 reference

23 September 2017

Frank Noé

series ordinal

2

1 reference

23 September 2017

language of work or name

English

0 references

publication date

2 July 2015

1 reference

23 September 2017

Nature Communications

1 reference

23 September 2017

6

1 reference

23 September 2017

7653

1 reference

Creative Commons Attribution 4.0 International

23 September 2017

start time

2 July 2015

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

exact match

https://scigraph.springernature.com/pub.10.1038/ncomms8653

0 references

cites work

EMMA: A Software Package for Markov Model Building and Analysis.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4506540

On-the-Fly Learning and Sampling of Ligand Binding by High-Throughput Molecular Simulations.

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4506540

Statistically optimal analysis of state-discretized trajectory data from multiple thermodynamic states

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4506540

Conformational selection in protein binding and function

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4506540

Quantitatively characterizing the ligand binding mechanisms of choline binding protein using Markov state model analysis

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4506540

Activation pathway of Src kinase reveals intermediate states as targets for drug design

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4506540

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

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4506540

ReaDDy--a software for particle-based reaction-diffusion dynamics in crowded cellular environments

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4506540

Enhanced modeling via network theory: Adaptive sampling of Markov state models

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4506540

Funnel metadynamics as accurate binding free-energy method

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4506540

Pharmacology and structure of isolated conformations of the adenosine A₂A receptor define ligand efficacy

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4506540

Kinetic characterization of the critical step in HIV-1 protease maturation

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4506540

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

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4506540

Conformational selection in trypsin-like proteases.

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4506540

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

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4506540

Structural basis for complement factor I control and its disease-associated sequence polymorphisms

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4506540

Allostery in trypsin-like proteases suggests new therapeutic strategies

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4506540

Crystallographic and Kinetic Evidence of Allostery in a Trypsin-like Protease

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4506540

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

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4506540

A role for both conformational selection and induced fit in ligand binding by the LAO protein

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4506540

From induced fit to conformational selection: a continuum of binding mechanism controlled by the timescale of conformational transitions

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4506540

Molecular simulation of ab initio protein folding for a millisecond folder NTL9(1-39)

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4506540

Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations.

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4506540

The role of dynamic conformational ensembles in biomolecular recognition

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4506540

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

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4506540

Structure of Human Prostasin, a Target for the Regulation of Hypertension

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4506540

Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4506540

Dynamic personalities of proteins

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4506540

Intrinsic dynamics of enzymes in the unbound state and relation to allosteric regulation

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4506540

Large-scale allosteric conformational transitions of adenylate kinase appear to involve a population-shift mechanism

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4506540

Pharmacogenetics and anti-arrhythmic drug therapy: a theoretical investigation

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4506540

Comparison of multiple Amber force fields and development of improved protein backbone parameters

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4506540

Application of a Theory of Enzyme Specificity to Protein Synthesis

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4506540

Fluctuating enzymes: lessons from single-molecule studies.

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4506540

Conformational lability in serine protease active sites: structures of hepatocyte growth factor activator (HGFA) alone and with the inhibitory domain from HGFA inhibitor-1B

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4506540

Development and testing of a general amber force field

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4506540

The many roles of computation in drug discovery

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4506540

Hit and lead generation: beyond high-throughput screening

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4506540

The 2.2-A crystal structure of human pro-granzyme K reveals a rigid zymogen with unusual features

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4506540

Crystal structure of a prostate kallikrein isolated from stallion seminal plasma: a homologue of human PSA

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4506540

The conformational plasticity of protein kinases

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4506540

The three-dimensional structure of Asp189Ser trypsin provides evidence for an inherent structural plasticity of the protease

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4506540

Structure of human factor D. A complement system protein at 2.0 A resolution

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4506540

Fast events in single-channel currents activated by acetylcholine and its analogues at the frog muscle end-plate

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4506540

Improvements in Markov State Model Construction Reveal Many Non-Native Interactions in the Folding of NTL9.

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4506540

Functional efficacy of adenosine A₂A receptor agonists is positively correlated to their receptor residence time

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4506540

X-ray structures of free and leupeptin-complexed human alphaI-tryptase mutants: indication for an alpha-->beta-tryptase transition

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4506540

Quantitative description of three modes of activity of fast chloride channels from rat skeletal muscle

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4506540

Perturbing the polar environment of Asp102 in trypsin: consequences of replacing conserved Ser214

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4506540

ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale.

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4506540

Kinetic modulation of a disordered protein domain by phosphorylation

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4506540

Fast recovery of free energy landscapes via diffusion-map-directed molecular dynamics.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4506540

Projected and hidden Markov models for calculating kinetics and metastable states of complex molecules

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4506540

Identification of slow molecular order parameters for Markov model construction

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4506540

A single-molecule dissection of ligand binding to a protein with intrinsic dynamics

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4506540

Markov models of molecular kinetics: generation and validation

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4506540

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

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4506540

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

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4506540

A coarse graining method for the identification of transition rates between molecular conformations.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4506540

Coarse master equation from Bayesian analysis of replica molecular dynamics simulations.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4506540

Error analysis and efficient sampling in Markovian state models for molecular dynamics.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4506540

Capillary force in atomic force microscopy

19 August 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS8653

Comparison of simple potential functions for simulating liquid water

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS8653

Fuzzy spectral clustering by PCCA+: application to Markov state models and data classification

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS8653

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

PubMed

https://pubmed.ncbi.nlm.nih.gov/26134632

12 December 2020

inferred from PubMed ID database lookup

STUDIES ON THE ACTIVE CENTER OF TRYPSIN. THE BINDING OF AMIDINES AND GUANIDINES AS MODELS OF THE SUBSTRATE SIDE CHAIN

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26134632

12 December 2020

inferred from PubMed ID database lookup

NMR characterization of the dynamics of biomacromolecules

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26134632

12 December 2020

inferred from PubMed ID database lookup

An Introduction to Markov State Models and Their Application to Long Timescale Molecular Simulation

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS8653

7 January 2021

inferred from DOI database lookup

The Jackknife and the Bootstrap for General Stationary Observations

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS8653

7 January 2021

inferred from DOI database lookup

Identifiers

DOI

10.1038/NCOMMS8653

1 reference

23 September 2017

0 references

1 reference

23 September 2017

PubMed publication ID

26134632

1 reference