(Q34292837)

1 August 2017

title

Protein loop modeling by using fragment assembly and analytical loop closure (English)

1 reference

1 August 2017

5

Chaok Seok

1 reference

1 August 2017

3

Hahnbeom Park

1 reference

1 August 2017

Julian Lee

1

1 reference

1 August 2017

Dongseon Lee

series ordinal

2

1 reference

1 August 2017

Evangelos A Coutsias

series ordinal

4

1 reference

1 August 2017

language of work or name

English

0 references

publication date

24 September 2010

1 reference

1 August 2017

number of pages

9

1 reference

based on heuristic

inferred from page(s)

published in

Proteins

1 reference

1 August 2017

volume

78

1 reference

1 August 2017

issue

16

1 reference

1 August 2017

page(s)

3428-3436

1 reference

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

1 August 2017

cites work

1 reference

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6 July 2018

1 reference

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Backbone statistical potential from local sequence-structure interactions in protein loops

6 July 2018

1 reference

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A self-organizing algorithm for modeling protein loops.

6 July 2018

1 reference

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

6 July 2018

1 reference

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Modeling protein loops with knowledge-based prediction of sequence-structure alignment.

6 July 2018

1 reference

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Shaping up the protein folding funnel by local interaction: lesson from a structure prediction study

6 July 2018

1 reference

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6 July 2018

1 reference

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Protein loop structure prediction with flexible stem geometries.

6 July 2018

1 reference

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Prediction of novel and analogous folds using fragment assembly and fold recognition.

6 July 2018

1 reference

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Assessment of CASP6 predictions for new and nearly new fold targets

6 July 2018

1 reference

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Critical assessment of methods of protein structure prediction (CASP)--round 6.

6 July 2018

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6 July 2018

1 reference

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Protein structure prediction based on fragment assembly and parameter optimization.

6 July 2018

1 reference

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Prediction of protein tertiary structure using PROFESY, a novel method based on fragment assembly and conformational space annealing

6 July 2018

1 reference

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6 July 2018

1 reference

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Protein structure prediction using Rosetta

6 July 2018

1 reference

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6 July 2018

1 reference

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Accurate and efficient loop selections by the DFIRE-based all-atom statistical potential.

6 July 2018

1 reference

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Predictions without templates: New folds, secondary structure, and contacts in CASP5

6 July 2018

1 reference

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Revisiting the Ramachandran plot: Hard‐sphere repulsion, electrostatics, and H‐bonding in the α‐helix

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2976774

Stereochemistry of polypeptide chain configurations

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2976774

A graph-theory algorithm for rapid protein side-chain prediction

6 July 2018

1 reference

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Cyclic coordinate descent: A robotics algorithm for protein loop closure.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2976774

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2976774

Protein structure prediction and structural genomics

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2976774

Modeling of loops in protein structures

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2976774

The ASTRAL compendium for protein structure and sequence analysis

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2976774

Protein secondary structure prediction based on position-specific scoring matrices

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2976774

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

6 July 2018

1 reference

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Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2976774

Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2976774

Backbone-dependent rotamer library for proteins. Application to side-chain prediction

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2976774

Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2976774

Improved Energy Selection of Nativelike Protein Loops from Loop Decoys.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2976774

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

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2976774

Protein-protein docking with backbone flexibility.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2976774

Long loop prediction using the protein local optimization program.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2976774

A methodology for efficiently sampling the conformation space of molecular structures.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2976774

Prediction of protein solvent accessibility using fuzzy k-nearest neighbor method.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2976774

Geometric algorithms for the conformational analysis of long protein loops

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2976774

A kinematic view of loop closure

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2976774

Ab initio construction of polypeptide fragments: efficient generation of accurate, representative ensembles.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2976774

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

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2976774

Predicting novel protein folds by using FRAGFOLD.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2976774

Assessment of novel fold targets in CASP4: predictions of three-dimensional structures, secondary structures, and interresidue contacts.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2976774

Protein folding using fragment assembly and physical energy function

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2976774

Prediction of the folding of short polypeptide segments by uniform conformational sampling

28 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20872556

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Predicting antibody hypervariable loop conformations. II: Minimization and molecular dynamics studies of MCPC603 from many randomly generated loop conformations

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20872556

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1002/PROT.22849

1 reference

1 August 2017

1 reference

1 August 2017

1 reference