(Q35822716)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26505632%20AND%20SRC:MED&resulttype=core&format=json

28 February 2020

title

ENCORE: Software for Quantitative Ensemble Comparison (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26505632%20AND%20SRC:MED&resulttype=core&format=json

28 February 2020

0 references

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26505632%20AND%20SRC:MED&resulttype=core&format=json

28 February 2020

Tone Bengtsen

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26505632%20AND%20SRC:MED&resulttype=core&format=json

28 February 2020

Wouter Boomsma

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26505632%20AND%20SRC:MED&resulttype=core&format=json

28 February 2020

Kresten Lindorff-Larsen

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26505632%20AND%20SRC:MED&resulttype=core&format=json

28 February 2020

author name string

Matteo Tiberti

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26505632%20AND%20SRC:MED&resulttype=core&format=json

28 February 2020

publication date

27 October 2015

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26505632%20AND%20SRC:MED&resulttype=core&format=json

PLOS Computational Biology

28 February 2020

published in

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26505632%20AND%20SRC:MED&resulttype=core&format=json

28 February 2020

volume

11

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26505632%20AND%20SRC:MED&resulttype=core&format=json

28 February 2020

issue

10

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26505632%20AND%20SRC:MED&resulttype=core&format=json

28 February 2020

page(s)

e1004415

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26505632%20AND%20SRC:MED&resulttype=core&format=json

Creative Commons Attribution 4.0 International

28 February 2020

copyright license

start time

27 October 2015

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Predicting the Thermodynamics and Kinetics of Helix Formation in a Cyclic Peptide Model.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4624683

E pluribus unum, no more: from one crystal, many conformations

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4624683

Markov state models of biomolecular conformational 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=4624683

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4624683

Bayesian energy landscape tilting: towards concordant models of molecular ensembles

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4624683

Inference of structure ensembles of flexible biomolecules from sparse, averaged data

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4624683

Comprehensive macromolecular conformations mapped by quantitative SAXS analyses

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4624683

On the statistical equivalence of restrained-ensemble simulations with the maximum entropy method

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4624683

Comparing Conformational Ensembles Using the Kullback-Leibler Divergence Expansion

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4624683

Systematic validation of protein force fields against experimental data

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4624683

How fast-folding proteins fold

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4624683

Tree preserving embedding

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4624683

Weak Long-Range Correlated Motions in a Surface Patch of Ubiquitin Involved in Molecular Recognition

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4624683

MDAnalysis: a toolkit for the analysis of molecular dynamics simulations

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4624683

Mixture models for protein structure ensembles.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4624683

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

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4624683

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

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4624683

Clustering by passing messages between data points

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4624683

Relation between native ensembles and experimental structures of proteins

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4624683

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

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4624683

Sensitivity and selectivity in protein structure comparison

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4624683

A self-organizing principle for learning nonlinear manifolds

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4624683

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

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4624683

On the Use of Experimental Observations to Bias Simulated Ensembles

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4624683

Surprisal Metrics for Quantifying Perturbed Conformational Dynamics in Markov State 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=4624683

Comparing molecular dynamics force fields in the essential subspace.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4624683

Combining experiments and simulations using the maximum entropy principle

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4624683

Improved Cross Validation of a Static Ubiquitin Structure Derived from High Precision Residual Dipolar Couplings Measured in a Drug-Based Liquid Crystalline Phase

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4624683

Phosphorylation drives a dynamic switch in serine/arginine-rich proteins

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4624683

Determination of structural fluctuations of proteins from structure-based calculations of residual dipolar couplings

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4624683

Fast large-scale clustering of protein structures using Gauss integrals

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4624683

Let's get honest about sampling.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4624683

Atomic-level characterization of the structural dynamics of proteins

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4624683

Fast mapping of global protein folding states by multivariate NMR: a GPS for proteins

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4624683

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4624683

Protein folding and the organization of the protein topology universe.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4624683

Simultaneous determination of protein structure and 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=4624683

Convergence of sampling in protein simulations.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4624683

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

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4624683

Cython: The Best of Both Worlds

24 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004415

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

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004415

Will molecular dynamics simulations of proteins ever reach equilibrium?

21 January 2018

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

Molecular dynamics simulations with replica-averaged structural restraints generate structural ensembles according to the maximum entropy principle

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.PCBI.1004415

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26505632%20AND%20SRC:MED&resulttype=core&format=json

journals/ploscb/TibertiPBBL15

28 February 2020

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

release_7d4cbwznurb6xpqiriv6ntwd7q

28 January 2021

Fatcat ID

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/7d4cbwznurb6xpqiriv6ntwd7q

24 November 2022

mapped directly with Wikidata item

0 references

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26505632%20AND%20SRC:MED&resulttype=core&format=json

28 February 2020

PubMed publication ID

26505632

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26505632%20AND%20SRC:MED&resulttype=core&format=json