(Q30416380)

14 October 2017

Towards the prediction of order parameters from molecular dynamics simulations in proteins (English)

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molecular dynamics simulation

14 October 2017

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author name string

Juan R Perilla

series ordinal

1

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14 October 2017

Thomas B Woolf

series ordinal

2

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14 October 2017

language of work or name

English

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publication date

1 April 2012

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Journal of Chemical Physics

14 October 2017

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14 October 2017

136

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14 October 2017

16

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14 October 2017

164101

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Molecular simulation approaches to membrane proteins.

14 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3350535

QAARM: quasi-anharmonic autoregressive model reveals molecular recognition pathways in ubiquitin

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3350535

Discovering conformational sub-states relevant to protein function

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3350535

Protein folded states are kinetic hubs

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3350535

Instantaneous normal modes as an unforced reaction coordinate for protein conformational transitions

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3350535

Molecular Basis of Alternating Access Membrane Transport by the Sodium-Hydantoin Transporter Mhp1

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3350535

A Comparison of Three Perturbation Molecular Dynamics Methods for Modeling Conformational Transitions

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3350535

Cooperative nature of gating transitions in K(+) channels as seen from dynamic importance sampling calculations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3350535

Zipping and unzipping of adenylate kinase: atomistic insights into the ensemble of open<-->closed transitions.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3350535

Extracting the causality of correlated motions from molecular dynamics simulations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3350535

Detection of functional modes in protein dynamics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3350535

Segmented transition pathway of the signaling protein nitrogen regulatory protein C

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3350535

CHARMM: the biomolecular simulation program

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3350535

Statistically optimal analysis of samples from multiple equilibrium states

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3350535

Conformational transition pathways explored by Monte Carlo simulation integrated with collective modes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3350535

Dynamic personalities of proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3350535

Efficient and verified simulation of a path ensemble for conformational change in a united-residue model of calmodulin.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3350535

Signal propagation in proteins and relation to equilibrium fluctuations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3350535

Conformational changes of glucose/galactose-binding protein illuminated by open, unliganded, and ultra-high-resolution ligand-bound structures

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3350535

Theoretical and computational models of biological ion channels

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3350535

Essential dynamics sampling study of adenylate kinase: comparison to citrate synthase and implication for the hinge and shear mechanisms of domain motions

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3350535

Scalable molecular dynamics with NAMD

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3350535

Large amplitude conformational change in proteins explored with a plastic network model: adenylate kinase

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3350535

Normal modes for predicting protein motions: a comprehensive database assessment and associated Web tool

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3350535

Normal-modes-based prediction of protein conformational changes guided by distance constraints

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3350535

Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3350535

ProMode: a database of normal mode analyses on protein molecules with a full-atom model.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3350535

A comparative study of motor-protein motions by using a simple elastic-network model

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3350535

Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3350535

High-resolution solution structure of the beryllofluoride-activated NtrC receiver domain

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3350535

Molecular dynamics simulations of peptides and proteins with amplified collective motions

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3350535

MolMovDB: analysis and visualization of conformational change and structural flexibility

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3350535

Conformational change of proteins arising from normal mode calculations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3350535

Measuring Information Transfer

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3350535

Reaction coordinates of biomolecular isomerization

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3350535

Structure of a transiently phosphorylated switch in bacterial signal transduction

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3350535

Solution conformations and thermodynamics of structured peptides: molecular dynamics simulation with an implicit solvation model.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3350535

The consistency of large concerted motions in proteins in molecular dynamics simulations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3350535

VMD: visual molecular dynamics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3350535

Essential dynamics of proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3350535

Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3350535

Dynamics of a small globular protein in terms of low-frequency vibrational modes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3350535

Projection of Monte Carlo and molecular dynamics trajectories onto the normal mode axes: human lysozyme

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3350535

Collective motions in proteins: A covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3350535

Probability Distributions for Complex Systems: Adaptive Umbrella Sampling of the Potential Energy

20 June 2018

1 reference

Use of the Weighted Histogram Analysis Method for the Analysis of Simulated and Parallel Tempering Simulations

21 January 2018

1 reference

THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method

21 January 2018

1 reference

Transition pathways in complex systems: Application of the finite-temperature string method to the alanine dipeptide

21 January 2018

1 reference

Protein conformational transitions explored by mixed elastic network models.

21 January 2018

1 reference

Computing ensembles of transitions from stable states: Dynamic importance sampling.

21 January 2018

1 reference

Efficient dynamic importance sampling of rare events in one dimension.

21 January 2018

1 reference

On Information and Sufficiency

21 January 2018

1 reference

Evaluating information transfer between auditory cortical neurons.

21 January 2018

1 reference

A symbolic representation of time series, with implications for streaming algorithms

21 January 2018

1 reference

Sampling protein conformations and pathways

21 January 2018

1 reference

Determination of reaction coordinates via locally scaled diffusion map.

21 January 2018

1 reference

Normal mode analysis for proteins

21 January 2018

1 reference

The essential dynamics of thermolysin: Confirmation of the hinge-bending motion and comparison of simulations in vacuum and water

21 January 2018

1 reference

Harmonicity and anharmonicity in protein dynamics: a normal mode analysis and principal component analysis

21 January 2018

1 reference

12 December 2020

Open-state conformation of the KcsA K+ channel: Monte Carlo normal mode following simulations

1 reference

12 December 2020

Symbolic transfer entropy

1 reference

12 December 2020

Elastic models of conformational transitions in macromolecules

1 reference

12 December 2020

Information transfer at multiple scales

1 reference

12 December 2020

Multiple pathways in conformational transitions of the alanine dipeptide: an application of dynamic importance sampling

1 reference

12 December 2020

Large-amplitude nonlinear motions in proteins

1 reference

12 December 2020

Two-state allosteric behavior in a single-domain signaling protein

1 reference

12 December 2020

Simulation of conformational transitions by the restricted perturbation-targeted molecular dynamics method

1 reference

12 December 2020

Full correlation analysis of conformational protein dynamics

1 reference

12 December 2020

Identifiers

DOI

10.1063/1.3702447

1 reference

14 October 2017

1 reference

14 October 2017

PubMed publication ID

22559464

1 reference