(Q39453313)

12 September 2017

Metadynamic metainference: Enhanced sampling of the metainference ensemble using metadynamics (English)

1 reference

12 September 2017

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27561930%20AND%20SRC:MED&resulttype=core&format=json

13 June 2020

Carlo Camilloni

series ordinal

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27561930%20AND%20SRC:MED&resulttype=core&format=json

13 June 2020

Michele Vendruscolo

series ordinal

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27561930%20AND%20SRC:MED&resulttype=core&format=json

13 June 2020

author name string

Massimiliano Bonomi

series ordinal

1

1 reference

12 September 2017

language of work or name

English

0 references

publication date

26 August 2016

1 reference

12 September 2017

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27561930%20AND%20SRC:MED&resulttype=core&format=json

13 June 2020

volume

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27561930%20AND%20SRC:MED&resulttype=core&format=json

13 June 2020

page(s)

31232

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27561930%20AND%20SRC:MED&resulttype=core&format=json

Creative Commons Attribution 4.0 International

13 June 2020

copyright license

start time

26 August 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

describes a project that uses

Bayes' theorem

1 reference

18 June 2022

https://europepmc.org/article/PMC/4999896

inferred from PubMed Central ID database lookup

exact match

https://scigraph.springernature.com/pub.10.1038/srep31232

0 references

cites work

Spectral gap optimization of order parameters for sampling complex molecular systems

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4999896

GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4999896

The molecular architecture of the Dam1 kinetochore complex is defined by cross-linking based structural modelling

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4999896

Architecture of the Human and Yeast General Transcription and DNA Repair Factor TFIIH

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4999896

Uncertainty in integrative structural modeling

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4999896

Molecular architecture of the 40S⋅eIF1⋅eIF3 translation initiation complex

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4999896

Determining protein complex structures based on a Bayesian model of in vivo Förster resonance energy transfer (FRET) data

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4999896

Cys-scanning disulfide crosslinking and bayesian modeling probe the transmembrane signaling mechanism of the histidine kinase, PhoQ.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4999896

Molecular architecture and function of the SEA complex, a modulator of the TORC1 pathway.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4999896

Design and application of implicit solvent models in biomolecular simulations

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4999896

The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4999896

Elucidating the mechanism of substrate recognition by the bacterial Hsp90 molecular chaperone

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4999896

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

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4999896

Biochemistry. Integrative structural biology

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4999896

Assembly of macromolecular complexes by satisfaction of spatial restraints from electron microscopy images

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4999896

Using sketch-map coordinates to analyze and bias molecular dynamics simulations

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4999896

Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4999896

Putting the pieces together: integrative modeling platform software for structure determination of macromolecular assemblies

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4999896

The three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4999896

Macromolecular docking restrained by a small angle X-ray scattering profile

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4999896

Integrative structure modeling of macromolecular assemblies from proteomics data

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4999896

Improved side-chain torsion potentials for the Amber ff99SB protein force field

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4999896

Insights into the molecular architecture of the 26S proteasome

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4999896

Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4999896

The molecular architecture of the nuclear pore complex

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4999896

The MARTINI force field: coarse grained model for biomolecular simulations

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4999896

A bias-exchange approach to protein folding

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4999896

Simultaneous determination of protein structure and dynamics.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4999896

Stereochemistry of polypeptide chain configurations

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4999896

Escaping free-energy minima

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4999896

Reaction coordinates of biomolecular isomerization

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4999896

Structure and dynamics of the integrin LFA-1 I-domain in the inactive state underlie its inside-out/outside-in signaling and allosteric mechanisms

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4999896

Metainference: A Bayesian inference method for heterogeneous systems

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4999896

Bayesian ensemble refinement by replica simulations and reweighting

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4999896

Replica-Averaged Metadynamics

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4999896

Efficient Sampling of High-Dimensional Free-Energy Landscapes with Parallel Bias Metadynamics.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4999896

A time-independent free energy estimator for metadynamics.

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4999896

Modeling of proteins and their assemblies with the Integrative Modeling Platform

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4999896

Metadynamics in the conformational space nonlinearly dimensionally reduced by Isomap.

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4999896

Reconstructing the equilibrium Boltzmann distribution from well-tempered metadynamics.

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4999896

Inferential optimization for simultaneous fitting of multiple components into a CryoEM map of their assembly

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4999896

From A to B in free energy space.

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4999896

Automatic method for identifying reaction coordinates in complex systems.

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4999896

String method in collective variables: minimum free energy paths and isocommittor surfaces.

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4999896

Efficient reconstruction of complex free energy landscapes by multiple walkers metadynamics.

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4999896

Inferential structure determination.

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4999896

Combining experiments and simulations using the maximum entropy principle

21 August 2018

1 reference

Crossref

https://api.crossref.org/works/10.1038%2FSREP31232

The role of water in host-guest interaction

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1038%2FSREP31232

Assessing the Quality of the OPEP Coarse-Grained Force Field

21 January 2018

1 reference

12 December 2020

Statistical mechanics of the denatured state of a protein using replica-averaged metadynamics

1 reference

12 December 2020

Optimized Monte Carlo data analysis

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

Identifiers

DOI

10.1038/SREP31232

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27561930%20AND%20SRC:MED&resulttype=core&format=json

Dimensions Publication ID

13 June 2020

0 references

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27561930%20AND%20SRC:MED&resulttype=core&format=json

13 June 2020

1 reference