Protein structure refinement via molecular-dynamics simulations: What works and what does not? (Q30377414)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26234208%20AND%20SRC:MED&resulttype=core&format=json

20 February 2020

title

Protein structure refinement via molecular-dynamics simulations: What works and what does not? (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26234208%20AND%20SRC:MED&resulttype=core&format=json

20 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26234208%20AND%20SRC:MED&resulttype=core&format=json

20 February 2020

Michael Feig

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26234208%20AND%20SRC:MED&resulttype=core&format=json

20 February 2020

language of work or name

English

0 references

publication date

17 August 2015

1 reference

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20 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26234208%20AND%20SRC:MED&resulttype=core&format=json

20 February 2020

volume

84 Suppl 1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26234208%20AND%20SRC:MED&resulttype=core&format=json

20 February 2020

page(s)

282-292

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26234208%20AND%20SRC:MED&resulttype=core&format=json

Significant Refinement of Protein Structure Models Using a Residue-Specific Force Field.

20 February 2020

cites work

1 reference

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The origin of consistent protein structure refinement from structural averaging.

20 June 2018

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

20 June 2018

1 reference

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Evaluation of unrestrained replica-exchange simulations using dynamic walkers in temperature space for protein structure refinement.

20 June 2018

1 reference

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Protein structure refinement of CASP target proteins using GNEIMO torsional dynamics method

20 June 2018

1 reference

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Assessment of template-based protein structure predictions in CASP10

20 June 2018

1 reference

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CASP10 results compared to those of previous CASP experiments

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5493977

Iterative Molecular Dynamics-Rosetta Protein Structure Refinement Protocol to Improve Model Quality.

20 June 2018

1 reference

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Evaluation of predictions in the CASP10 model refinement category.

20 June 2018

1 reference

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GalaxyRefine: Protein structure refinement driven by side-chain repacking

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5493977

Physics-based protein structure refinement through multiple molecular dynamics trajectories and structure averaging

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5493977

Protein Structure Refinement through Structure Selection and Averaging from Molecular Dynamics Ensembles.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5493977

Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ(1) and χ(2) dihedral angles

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5493977

GRID: a high-resolution protein structure refinement algorithm

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5493977

3Drefine: consistent protein structure refinement by optimizing hydrogen bonding network and atomic-level energy minimization

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5493977

Accurate de novo structure prediction of large transmembrane protein domains using fragment-assembly and correlated mutation analysis

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5493977

KoBaMIN: a knowledge-based minimization web server for protein structure refinement

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5493977

AWSEM-MD: protein structure prediction using coarse-grained physical potentials and bioinformatically based local structure biasing

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5493977

Refinement of unreliable local regions in template-based protein models

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5493977

Automated protein structure modeling in CASP9 by I-TASSER pipeline combined with QUARK-based ab initio folding and FG-MD-based structure refinement

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5493977

Assessment of protein structure refinement in CASP9.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5493977

How fast-folding proteins fold

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5493977

A novel side-chain orientation dependent potential derived from random-walk reference state for protein fold selection and structure prediction

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5493977

MolProbity: all-atom structure validation for macromolecular crystallography

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5493977

Protein structure prediction: when is it useful?

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5493977

Sampling of near-native protein conformations during protein structure refinement using a coarse-grained model, normal modes, and 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=5493977

Can molecular dynamics simulations provide high-resolution refinement of protein structure?

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5493977

Near-native structure refinement using in vacuo energy minimization.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5493977

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=5493977

MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology.

20 June 2018

1 reference

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Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5493977

Accurate reconstruction of all-atom protein representations from side-chain-based low-resolution models

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5493977

Comparison between self-guided Langevin dynamics and molecular dynamics simulations for structure refinement of protein loop conformations

20 June 2018

1 reference

Crossref

https://api.crossref.org/works/10.1002%2FPROT.24871

Refinement of protein termini in template-based modeling using conformational space annealing

21 January 2018

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Crossref

https://api.crossref.org/works/10.1002%2FPROT.24871

Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems

21 January 2018

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https://api.crossref.org/works/10.1002%2FPROT.24871

Application of statistical potentials to protein structure refinement from low resolution ab initio models

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26234208

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1002/PROT.24871

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26234208%20AND%20SRC:MED&resulttype=core&format=json

20 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26234208%20AND%20SRC:MED&resulttype=core&format=json

20 February 2020

PubMed publication ID

26234208

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26234208%20AND%20SRC:MED&resulttype=core&format=json