(Q30368895)

13 October 2017

Protein loop modeling using a new hybrid energy function and its application to modeling in inaccurate structural environments. (English)

1 reference

13 October 2017

4

Chaok Seok

1 reference

13 October 2017

Lim Heo

3

0 references

Hahnbeom Park

series ordinal

1

object named as

Hahnbeom Park

1 reference

13 October 2017

2

Gyu Rie Lee

1 reference

PMC publication ID

4242723

13 October 2017

language of work or name

English

0 references

publication date

24 November 2014

1 reference

13 October 2017

1 reference

13 October 2017

9

1 reference

13 October 2017

11

1 reference

13 October 2017

e113811

1 reference

Creative Commons Attribution 4.0 International

13 October 2017

start time

24 November 2014

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4242723

Improvements to robotics-inspired conformational sampling in rosetta

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4242723

LoopWeaver: loop modeling by the weighted scaling of verified proteins

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4242723

Incorporating backbone flexibility in MedusaDock improves ligand-binding pose prediction in the CSAR2011 docking benchmark

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4242723

SALIGN: a web server for alignment of multiple protein sequences and structures

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4242723

Refinement of unreliable local regions in template-based protein models

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4242723

Structure prediction of loops with fixed and flexible stems

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4242723

Assessment of template based protein structure predictions in CASP9.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4242723

The FALC-Loop web server for protein loop modeling

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4242723

Improved molecular replacement by density- and energy-guided protein structure optimization

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4242723

Development of a new physics‐based internal coordinate mechanics force field and its application to protein loop modeling

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4242723

Protein loop modeling by using fragment assembly and analytical loop closure

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4242723

Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4242723

Loop modeling: Sampling, filtering, and scoring

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4242723

Comparison of multiple Amber force fields and development of improved protein backbone parameters

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4242723

Soft docking and multiple receptor conformations in virtual screening

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4242723

Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4242723

A hierarchical approach to all-atom protein loop prediction

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4242723

Alignment of protein sequences by their profiles

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4242723

ModLoop: automated modeling of loops in protein structures

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4242723

Free energy landscape of protein folding in water: Explicit vs. implicit solvent

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4242723

Can a continuum solvent model reproduce the free energy landscape of a beta -hairpin folding in water?

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4242723

Modeling of loops in protein structures

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4242723

A single-domain antibody fragment in complex with RNase A: non-canonical loop structures and nanomolar affinity using two CDR loops

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4242723

Energy-based de novo protein folding by conformational space annealing and an off-lattice united-residue force field: application to the 10-55 fragment of staphylococcal protein A and to apo calbindin D9K.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4242723

HOMSTRAD: a database of protein structure alignments for homologous families

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4242723

Subtle hydrophobic interactions between the seventh residue of the zinc finger loop and the first base of an HGATAR sequence determine promoter-specific recognition by the Aspergillus nidulans GATA factor AreA.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4242723

Comparative protein modelling by satisfaction of spatial restraints

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4242723

The P-loop--a common motif in ATP- and GTP-binding proteins

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4242723

Modeling the anti-CEA antibody combining site by homology and conformational search

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4242723

Protein-protein docking with backbone flexibility.

3 June 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0113811

Ab initio construction of polypeptide fragments: Accuracy of loop decoy discrimination by an all-atom statistical potential and the AMBER force field with the Generalized Born solvation model

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0113811

Protein Loop Modeling with Optimized Backbone Potential Functions.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0113811

Remarkable loop flexibility in avian influenza N1 and its implications for antiviral drug design.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0113811

Toward better refinement of comparative models: predicting loops in inexact environments

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0113811

The SGB/NP hydration free energy model based on the surface generalized born solvent reaction field and novel nonpolar hydration free energy estimators

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0113811

Investigation of Salt Bridge Stability in a Generalized Born Solvent Model.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0113811

Ensemble docking into flexible active sites. Critical evaluation of FlexE against JNK-3 and beta-secretase.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0113811

Long loop prediction using the protein local optimization program.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0113811

Semianalytical treatment of solvation for molecular mechanics and dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0113811

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0113811

FACTS: Fast analytical continuum treatment of solvation.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0113811

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/10.1371%2FJOURNAL.PONE.0113811

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0113811

A kinematic view of loop closure

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0113811

Force Field Validation Using Protein Side Chain Prediction

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0113811

10.1371/JOURNAL.PONE.0113811

21 January 2018

Identifiers

DOI

1 reference

13 October 2017

0 references

1 reference

PMC publication ID

4242723

13 October 2017

PubMed publication ID

25419655

1 reference

PMC publication ID

4242723