GalaxyRefine: Protein structure refinement driven by side-chain repacking (Q30431476)

17 August 2017

GalaxyRefine: Protein structure refinement driven by side-chain repacking (English)

1 reference

17 August 2017

3

Chaok Seok

1 reference

17 August 2017

2

Hahnbeom Park

1 reference

17 August 2017

1

Lim Heo

1 reference

PMCID

3692086

17 August 2017

language of work or name

English

0 references

publication date

3 June 2013

1 reference

17 August 2017

Nucleic Acids Research

1 reference

17 August 2017

41

1 reference

17 August 2017

W384-8

1 reference

17 August 2017

Web Server issue

1 reference

Creative Commons Attribution 3.0 Unported

17 August 2017

start time

4 October 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

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1 reference

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GalaxyDock: protein-ligand docking with flexible protein side-chains

20 June 2018

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

20 June 2018

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GalaxyTBM: template-based modeling by building a reliable core and refining unreliable local regions

20 June 2018

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GalaxyWEB server for protein structure prediction and refinement

20 June 2018

1 reference

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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=3692086

Refinement of unreliable local regions in template-based protein models

20 June 2018

1 reference

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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=3692086

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

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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=3692086

CASP9 assessment of free modeling target predictions

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3692086

The FALC-Loop web server for protein loop modeling

20 June 2018

1 reference

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ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3692086

Protein loop modeling by using fragment assembly and analytical loop closure

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3692086

I-TASSER: a unified platform for automated protein structure and function prediction

20 June 2018

1 reference

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MolProbity: all-atom structure validation for macromolecular crystallography

20 June 2018

1 reference

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Assessment of CASP8 structure predictions for template free 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=3692086

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=3692086

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=3692086

Structure prediction for CASP8 with all-atom refinement using Rosetta.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3692086

Scoring function for automated assessment of protein structure template quality

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3692086

A graph-theory algorithm for rapid protein side-chain 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=3692086

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

20 June 2018

1 reference

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Rotamer libraries in the 21st century

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3692086

Comparative protein structure modeling of genes and genomes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3692086

CASP9 results compared to those of previous CASP experiments

20 June 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKT458

A kinematic view of loop closure.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKT458

FACTS: Fast analytical continuum treatment of solvation.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKT458

An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKT458

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKT458

GalaxyGemini: a web server for protein homo-oligomer structure prediction based on similarity

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23737448

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/NAR/GKT458

1 reference

17 August 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

17 August 2017

1 reference

PMCID

3692086