(Q43211258)

16 November 2017

Similarity measures for protein ensembles (English)

1 reference

16 November 2017

Kresten Lindorff-Larsen

series ordinal

1

1 reference

PMCID

2615214

16 November 2017

Jesper Ferkinghoff-Borg

series ordinal

2

object named as

Jesper Ferkinghoff-Borg

1 reference

PMCID

2615214

16 November 2017

language of work or name

English

0 references

publication date

15 January 2009

1 reference

16 November 2017

1 reference

16 November 2017

4

1 reference

16 November 2017

1

1 reference

16 November 2017

e4203

1 reference

Creative Commons Attribution 4.0 International

16 November 2017

start time

15 January 2009

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

All-atom empirical potential for molecular modeling and dynamics studies of proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615214

Ensemble Refinement of Protein Crystal Structures: Validation and Application

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615214

Protein structural variation in computational models and crystallographic data

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615214

The MUMO (minimal under-restraining minimal over-restraining) method for the determination of native state ensembles of proteins

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615214

Clustering by passing messages between data points

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615214

A consensus view of protein dynamics

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615214

The dynamic energy landscape of dihydrofolate reductase catalysis

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615214

Relation between native ensembles and experimental structures of proteins

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615214

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

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615214

Ensemble-based convergence analysis of biomolecular trajectories

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615214

Comparing atomistic simulation data with the NMR experiment: how much can NOEs actually tell us?

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615214

Quantifying allosteric effects in proteins.

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615214

Protein folding and the organization of the protein topology universe.

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615214

Simultaneous determination of protein structure and dynamics.

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615214

Heterogeneity and inaccuracy in protein structures solved by X-ray crystallography.

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615214

Sensitivity and selectivity in protein structure comparison

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615214

The role of dynamics in allosteric regulation

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615214

Structural genomics: computational methods for structure analysis

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615214

A global representation of the protein fold space

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615214

A self-organizing principle for learning nonlinear manifolds

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615214

Molecular dynamics simulations of biomolecules

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615214

Forced unfolding of fibronectin type 3 modules: an analysis by biased molecular dynamics simulations

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615214

Investigating protein dynamics in collective coordinate space

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615214

Effective energy function for proteins in solution

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615214

Molecular dynamics and accuracy of NMR structures: effects of error bounds and data removal

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615214

Influence of internal dynamics on accuracy of protein NMR structures: derivation of realistic model distance data from a long molecular dynamics trajectory.

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615214

Do NOE distances contain enough information to assess the relative populations of multi-conformer structures?

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615214

Direct observation of protein solvation and discrete disorder with experimental crystallographic phases

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615214

Essential dynamics of proteins

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615214

Quality Assurance for Biomolecular Simulations.

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615214

Statistical characterization of protein ensembles.

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615214

Accurate ranking of differentially expressed genes by a distribution-free shrinkage approach.

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615214

Statistical validation of the root-mean-square-distance, a measure of protein structural proximity.

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615214

Simulation studies of the fidelity of biomolecular structure ensemble recreation

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615214

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615214

A shrinkage approach to large-scale covariance matrix estimation and implications for functional genomics.

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615214

Inferential structure determination.

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615214

Cutoff size need not strongly influence molecular dynamics results for solvated polypeptides

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615214

Improved treatment of the protein backbone in empirical force fields.

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615214

Generalized born model with a simple smoothing function.

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615214

Convergence of sampling in protein simulations.

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615214

Relative entropy: free energy associated with equilibrium fluctuations and nonequilibrium deviations.

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615214

A global geometric framework for nonlinear dimensionality reduction

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615214

On Information and Sufficiency

15 August 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0004203

An invariant form for the prior probability in estimation problems

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0004203

Divergence measures based on the Shannon entropy

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0004203

A new class of metric divergences on probability spaces and its applicability in statistics

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0004203

On Estimation of a Probability Density Function and Mode

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0004203

Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0004203

Comparison of simple potential functions for simulating liquid water

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0004203

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0004203

Exploration of disorder in protein structures by X-ray restrained molecular dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0004203

Conformational Variability of Solution Nucelar Magnetic Resonance Structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0004203

Concordance of residual dipolar couplings, backbone order parameters and crystallographic B-factors for a small alpha/beta protein: a unified picture of high probability, fast atomic motions in proteins

21 January 2018

1 reference

12 December 2020

1 reference

12 December 2020

Is one solution good enough?

1 reference

12 December 2020

Molecular dynamics of native protein. II. Analysis and nature of motion

1 reference

12 December 2020

Internal motional averaging and three-dimensional structure determination by nuclear magnetic resonance

1 reference

12 December 2020

Increased protein backbone conformational entropy upon hydrophobic ligand binding

1 reference

12 December 2020

Convergence of molecular dynamics simulations of membrane proteins

1 reference

12 December 2020

Efficient RMSD measures for the comparison of two molecular ensembles. Root-mean-square deviation

1 reference

12 December 2020

10.1371/JOURNAL.PONE.0004203

Identifiers

DOI

1 reference

16 November 2017

0 references

1 reference

16 November 2017

1 reference

PMCID

2615214