Protein Structure Refinement through Structure Selection and Averaging from Molecular Dynamics Ensembles. (Q30428682)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23526422%20AND%20SRC:MED&resulttype=core&format=json

27 February 2020

title

Protein Structure Refinement through Structure Selection and Averaging from Molecular Dynamics Ensembles (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23526422%20AND%20SRC:MED&resulttype=core&format=json

molecular dynamics simulation

27 February 2020

main subject

0 references

0 references

1 reference

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27 February 2020

Michael Feig

1 reference

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27 February 2020

publication date

22 December 2012

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23526422%20AND%20SRC:MED&resulttype=core&format=json

Journal of Chemical Theory and Computation

27 February 2020

published in

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27 February 2020

volume

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27 February 2020

issue

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27 February 2020

page(s)

1294-1303

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23526422%20AND%20SRC:MED&resulttype=core&format=json

Assessment of Detection and Refinement Strategies for de novo Protein Structures Using Force Field and Statistical Potentials

27 February 2020

cites work

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20 June 2018

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Solvent dramatically affects protein structure refinement.

20 June 2018

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Protein model refinement using an optimized physics-based all-atom force field

20 June 2018

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Ab initio folding of terminal segments with secondary structures reveals the fine difference between two closely related all-atom statistical energy functions

20 June 2018

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Refining homology models by combining replica-exchange molecular dynamics and statistical potentials

20 June 2018

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20 June 2018

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20 June 2018

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Sampling of near-native protein conformations during protein structure refinement using a coarse-grained model, normal modes, and molecular dynamics simulations.

20 June 2018

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

20 June 2018

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20 June 2018

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20 June 2018

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Structural refinement of protein segments containing secondary structure elements: Local sampling, knowledge-based potentials, and clustering

20 June 2018

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20 June 2018

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20 June 2018

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20 June 2018

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20 June 2018

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20 June 2018

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20 June 2018

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20 June 2018

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20 June 2018

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20 June 2018

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20 June 2018

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20 June 2018

1 reference

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Molecular dynamics in the endgame of protein 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=3603382

Processing and analysis of CASP3 protein structure predictions

20 June 2018

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

20 June 2018

1 reference

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Comparative protein modelling by satisfaction of spatial restraints

20 June 2018

1 reference

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3603382

Exploring the potential of template-based modelling

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3603382

Specific interactions for ab initio folding of protein terminal regions with secondary structures.

26 November 2018

1 reference

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A correlation-based method for the enhancement of scoring functions on funnel-shaped energy landscapes.

26 November 2018

1 reference

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Improved treatment of the protein backbone in empirical force fields.

26 November 2018

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

26 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23526422

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

3D‐SHOTGUN: A novel, cooperative, fold‐recognition meta‐predictor

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23526422

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1021/CT300962X

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23526422%20AND%20SRC:MED&resulttype=core&format=json

27 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23526422%20AND%20SRC:MED&resulttype=core&format=json

27 February 2020

PubMed publication ID

23526422

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23526422%20AND%20SRC:MED&resulttype=core&format=json