(Q30352482)

16 October 2017

Evaluation of predictions in the CASP10 model refinement category. (English)

1 reference

16 October 2017

2

0 references

David Tudor Jones

series ordinal

3

object named as

David T Jones

1 reference

16 October 2017

Timothy Nugent

1

1 reference

PMC publication ID

4282348

16 October 2017

language of work or name

English

0 references

publication date

3 January 2014

1 reference

16 October 2017

1 reference

16 October 2017

82 Suppl 2

1 reference

16 October 2017

98-111

1 reference

FlexE: Using elastic network models to compare models of protein structure.

16 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282348

CASP prediction center infrastructure and evaluation measures in CASP10 and CASP ROLL.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282348

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=4282348

The RCSB Protein Data Bank: new resources for research and education

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282348

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=4282348

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=4282348

Significant reduction in errors associated with nonbonded contacts in protein crystal structures: automated all-atom refinement with PrimeX.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282348

GalaxyWEB server for protein structure prediction and 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=4282348

Elastic network normal modes provide a basis 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=4282348

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=4282348

Refinement of protein structure homology models via long, all-atom 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=4282348

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=4282348

Mimicking the action of folding chaperones by Hamiltonian replica-exchange molecular dynamics simulations: application in the refinement of de novo 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=4282348

Structure refinement of protein low resolution models using the GNEIMO constrained dynamics method

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282348

Atomic-level protein structure refinement using fragment-guided molecular dynamics conformation sampling

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282348

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=4282348

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=4282348

Reliable protein structure refinement using a physical energy function

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282348

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=4282348

The other 90% of the protein: assessment beyond the Calphas for CASP8 template-based and high-accuracy 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=4282348

Assessment of the protein-structure refinement category in CASP8

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282348

Phasercrystallographic software

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282348

Assessment of CASP7 predictions for template-based modeling targets

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282348

ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282348

LGA: A method for finding 3D similarities in protein structures

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282348

Pushing the boundaries of molecular replacement with maximum likelihood

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282348

Satisfying hydrogen bonding potential in proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4282348

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

20 June 2018

1 reference

Crossref

https://api.crossref.org/works/10.1002%2FPROT.24377

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

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1002%2FPROT.24377

Structure refinement of protein model decoys requires accurate side-chain placement

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23900810

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1002/PROT.24377

1 reference

16 October 2017

1 reference

PMC publication ID

4282348

16 October 2017

PubMed publication ID

23900810

1 reference

PMC publication ID

4282348