REMO: A new protocol to refine full atomic protein models from C-alpha traces by optimizing hydrogen-bonding networks (Q30375449)

20 August 2017

REMO: A new protocol to refine full atomic protein models from C-alpha traces by optimizing hydrogen-bonding networks (English)

1 reference

20 August 2017

Yunqi Li

1

1 reference

PMCID

2771173

20 August 2017

Yang Zhang

series ordinal

2

1 reference

PMCID

2771173

20 August 2017

language of work or name

English

0 references

publication date

1 August 2009

1 reference

20 August 2017

1 reference

20 August 2017

76

1 reference

20 August 2017

665-676

1 reference

20 August 2017

3

1 reference

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

20 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2771173

Progress and challenges in 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=2771173

MUSTER: Improving protein sequence profile-profile alignments by using multiple sources of structure information

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2771173

Fast procedure for reconstruction of full-atom protein models from reduced representations.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2771173

Template-based modeling and free modeling by I-TASSER in CASP7.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2771173

Automated server predictions in CASP7

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2771173

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=2771173

Ab initio modeling of small proteins by iterative TASSER 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=2771173

LOMETS: a local meta-threading-server for 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=2771173

Assessment of predictions submitted for the CASP6 comparative modeling category

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2771173

Physics-based protein-structure prediction using a hierarchical protocol based on the UNRES force field: assessment in two blind tests.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2771173

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=2771173

Tertiary structure predictions on a comprehensive benchmark of medium to large size 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=2771173

Automated structure prediction of weakly homologous proteins on a genomic scale

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2771173

SPICKER: a clustering approach to identify near-native protein folds

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2771173

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=2771173

TOUCHSTONE II: a new approach to ab initio 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=2771173

Local energy landscape flattening: parallel hyperbolic Monte Carlo sampling of protein folding.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2771173

Protein secondary structure prediction based on position-specific scoring matrices

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2771173

Clustering of low-energy conformations near the native structures of small 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=2771173

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2771173

Knowledge-based protein secondary structure assignment

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2771173

Comparative protein modelling by satisfaction of spatial restraints

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2771173

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=2771173

Database algorithm for generating protein backbone and side-chain co-ordinates from a C alpha trace application to model building and detection of co-ordinate errors.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2771173

A solution for the best rotation to relate two sets of vectors

20 June 2018

1 reference

Crossref

https://api.crossref.org/works/10.1002%2FPROT.22380

TASSER: an automated method for the prediction of protein tertiary structures in CASP6.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2771173

Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins

26 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19274737

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Using multiple structure alignments, fast model building, and energetic analysis in fold recognition and homology modeling

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19274737

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/19274737

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1002/PROT.22380

1 reference

20 August 2017

1 reference

20 August 2017

1 reference

PMCID

2771173