(Q33603623)

28 July 2017

title

Algorithmic dimensionality reduction for molecular structure analysis (English)

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28 July 2017

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dimensionality reduction

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Sara N Pollock

3

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Evangelos A. Coutsias

object named as

Evangelos A Coutsias

4

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author name string

W Michael Brown

1

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28 July 2017

Shawn Martin

2

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28 July 2017

Jean-Paul Watson

5

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28 July 2017

language of work or name

English

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publication date

1 August 2008

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Journal of Chemical Physics

28 July 2017

published in

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28 July 2017

volume

129

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28 July 2017

issue

6

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28 July 2017

page(s)

064118

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Multiscale simulation of soft matter: from scale bridging to adaptive resolution

28 July 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2809693

Reducing the dimensionality of data with neural networks

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2809693

Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2809693

Docking essential dynamics eigenstructures

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2809693

Fluctuations and correlations in crystalline protein dynamics: a simulation analysis of staphylococcal nuclease

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2809693

Improvement of comparative model accuracy by free-energy optimization along principal components of natural structural variation.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2809693

Theory of protein folding

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2809693

A self-organizing principle for learning nonlinear manifolds

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2809693

Molecular dynamics and NMR spin relaxation in proteins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2809693

Nonlinear dimensionality reduction by locally linear embedding

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2809693

The Flory isolated-pair hypothesis is not valid for polypeptide chains: implications for protein folding

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2809693

Understanding protein folding via free-energy surfaces from theory and experiment

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2809693

Investigating protein dynamics in collective coordinate space

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2809693

Domain motions in bacteriophage T4 lysozyme: a comparison between molecular dynamics and crystallographic data.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2809693

Locally accessible conformations of proteins: multiple molecular dynamics simulations of crambin

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2809693

Protein dynamics derived from clusters of crystal structures

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2809693

An extended sampling of the configurational space of HPr from E. coli.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2809693

An efficient method for sampling the essential subspace of proteins.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2809693

Essential dynamics of proteins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2809693

A sampling problem in molecular dynamics simulations of macromolecules

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2809693

Efficient Monte Carlo method for simulation of fluctuating conformations of native proteins.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2809693

Dominant forces in protein folding

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2809693

How complex is the dynamics of Peptide folding?

21 June 2018

1 reference

Can principal components yield a dimension reduced description of protein dynamics on long time scales?

21 January 2018

1 reference

Essential dynamics of reversible peptide folding: memory-free conformational dynamics governed by internal hydrogen bonds.

21 January 2018

1 reference

Efficient sampling in collective coordinate space.

21 January 2018

1 reference

Automatic identification of discrete substates in proteins: singular value decomposition analysis of time-averaged crystallographic refinements.

21 January 2018

1 reference

Dynamics of essential collective motions in proteins: theory

21 January 2018

1 reference

Collective Langevin dynamics of conformational motions in proteins.

21 January 2018

1 reference

Metadynamics in essential coordinates: free energy simulation of conformational changes.

21 January 2018

1 reference

Rapid protein-ligand docking using soft modes from molecular dynamics simulations to account for protein deformability: binding of FK506 to FKBP.

21 January 2018

1 reference

Dihedral angle principal component analysis of molecular dynamics simulations.

21 January 2018

1 reference

Complexity of free energy landscapes of peptides revealed by nonlinear principal component analysis.

21 January 2018

1 reference

A global geometric framework for nonlinear dimensionality reduction

21 January 2018

1 reference

Molecular geometry. V. Evaluation of functions and conformations of medium rings

21 January 2018

1 reference

Computation of the pseudorotation matrix to satisfy the Eckart axis conditions.

21 January 2018

1 reference

Functionally relevant protein motions: extracting basin-specific collective coordinates from molecular dynamics trajectories

21 January 2018

1 reference

A kinematic view of loop closure

21 January 2018

1 reference

Complete maps of molecular-loop conformational spaces.

21 January 2018

1 reference

Collective variable description of native protein dynamics

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2809693

30 October 2018

1 reference

Unfolded, yes, but random? Never!

21 January 2018

1 reference

Generalized correlation for biomolecular dynamics

21 January 2018

1 reference

12 December 2020

Collective NMR relaxation model applied to protein dynamics

1 reference

12 December 2020

A kinetic model for the internal motions of proteins: diffusion between multiple harmonic wells

1 reference

12 December 2020

Interaction potentials for soft and hard ellipsoids

1 reference

12 December 2020

Understanding protein flexibility through dimensionality reduction

1 reference

12 December 2020

Identifiers

DOI

10.1063/1.2968610

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28 July 2017

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28 July 2017

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