(Q30386605)

English

Contact prediction for beta and alpha-beta proteins using integer linear optimization and its impact on the first principles 3D structure prediction method ASTRO-FOLD.

scientific article

In more languages

Statements

scholarly article

1 reference

Europe PubMed Central

PMC publication ID

17 September 2017

Contact prediction for beta and alpha-beta proteins using integer linear optimization and its impact on the first principles 3D structure prediction method ASTRO-FOLD. (English)

1 reference

Europe PubMed Central

PMC publication ID

17 September 2017

protein folding

0 references

protein structure prediction

0 references

author name string

R Rajgaria

1

1 reference

Europe PubMed Central

PMC publication ID

17 September 2017

Y Wei

2

1 reference

Europe PubMed Central

PMC publication ID

17 September 2017

C A Floudas

3

1 reference

Europe PubMed Central

PMC publication ID

17 September 2017

language of work or name

0 references

publication date

1 June 2010

1 reference

Europe PubMed Central

PMC publication ID

17 September 2017

1 reference

Europe PubMed Central

PMC publication ID

17 September 2017

78

1 reference

Europe PubMed Central

PMC publication ID

17 September 2017

8

1 reference

Europe PubMed Central

PMC publication ID

17 September 2017

1825-1846

1 reference

Europe PubMed Central

PMC publication ID

17 September 2017

Enhanced Bounding Techniques to Reduce the Protein Conformational Search Space

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2858251

20 June 2018

An improved hybrid global optimization method for protein tertiary structure prediction

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2858251

20 June 2018

Selecting high quality protein structures from diverse conformational ensembles.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2858251

20 June 2018

Towards accurate residue-residue hydrophobic contact prediction for alpha helical proteins via integer linear optimization

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2858251

20 June 2018

Reconstruction of 3D structures from protein contact maps

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2858251

20 June 2018

Progress and challenges in protein structure prediction

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2858251

20 June 2018

A comprehensive assessment of sequence-based and template-based methods for protein contact prediction

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2858251

20 June 2018

Correlated substitution analysis and the prediction of amino acid structural contacts.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2858251

20 June 2018

Assessment of intramolecular contact predictions for CASP7.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2858251

20 June 2018

Computational methods in protein structure prediction.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2858251

20 June 2018

Improved residue contact prediction using support vector machines and a large feature set.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2858251

20 June 2018

Predicting residue contacts using pragmatic correlated mutations method: reducing the false positives

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2858251

20 June 2018

Novel approach for alpha-helical topology prediction in globular proteins: generation of interhelical restraints.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2858251

20 June 2018

A two-stage approach for improved prediction of residue contact maps.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2858251

20 June 2018

Protein loop structure prediction with flexible stem geometries.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2858251

20 June 2018

CASP6 assessment of contact prediction.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2858251

20 June 2018

PROFcon: novel prediction of long-range contacts.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2858251

20 June 2018

Ab initio prediction of the three-dimensional structure of a de novo designed protein: a double-blind case study

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2858251

20 June 2018

Scoring function for automated assessment of protein structure template quality

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2858251

20 June 2018

ASTRO-FOLD: A Combinatorial and Global Optimization Framework for Ab Initio Prediction of Three-Dimensional Structures of Proteins from the Amino Acid Sequence

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2858251

20 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2858251

20 June 2018

Hybrid global optimization algorithms for protein structure prediction: alternating hybrids

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2858251

20 June 2018

Prediction of protein residue contacts with a PDB-derived likelihood matrix.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2858251

20 June 2018

Prediction of contact maps by GIOHMMs and recurrent neural networks using lateral propagation from all four cardinal corners.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2858251

20 June 2018

Contact order and ab initio protein structure prediction

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2858251

20 June 2018

Comparative protein structure modeling of genes and genomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2858251

20 June 2018

Effective use of sequence correlation and conservation in fold recognition

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2858251

20 June 2018

Processing and analysis of CASP3 protein structure predictions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2858251

20 June 2018

Protein secondary structure prediction based on position-specific scoring matrices

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2858251

20 June 2018

A neural network based predictor of residue contacts in proteins.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2858251

20 June 2018

New developments of the electrostatically driven Monte Carlo method: test on the membrane-bound portion of melittin

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2858251

20 June 2018

Conformational analysis of the 20-residue membrane-bound portion of melittin by conformational space annealing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2858251

20 June 2018

Tertiary structure prediction of the KIX domain of CBP using Monte Carlo simulations driven by restraints derived from multiple sequence alignments

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2858251

20 June 2018

Fold assembly of small proteins using monte carlo simulations driven by restraints derived from multiple sequence alignments.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2858251

20 June 2018

Protein distance constraints predicted by neural networks and probability density functions.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2858251

20 June 2018

Nativelike topology assembly of small proteins using predicted restraints in Monte Carlo folding simulations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2858251

20 June 2018

Redefining the goals of protein secondary structure prediction

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2858251

20 June 2018

Comparative protein modelling by satisfaction of spatial restraints

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2858251

20 June 2018

Correlated mutations and residue contacts in proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2858251

20 June 2018

Compensating changes in protein multiple sequence alignments

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2858251

20 June 2018

SCOP: a structural classification of proteins database for the investigation of sequences and structures

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2858251

20 June 2018

Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2858251

20 June 2018

Hydrophobicity scales and computational techniques for detecting amphipathic structures in proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2858251

20 June 2018

Antiparallel and parallel β-strands differ in amino acid residue preferences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2858251

20 June 2018

Progress in predicting inter-residue contacts of proteins with neural networks and correlated mutations.

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22696

21 January 2018

Contact prediction using mutual information and neural nets

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2858251

26 November 2018

Separating true positive predicted residue contacts from false positive ones in mainly alpha proteins, using constrained Metropolis MC simulations.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2858251

26 November 2018

A novel high resolution Calpha--Calpha distance dependent force field based on a high quality decoy set.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2858251

26 November 2018

Prediction of inter-residue contacts map based on genetic algorithm optimized radial basis function neural network and binary input encoding scheme.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2858251

26 November 2018

Prediction of distant residue contacts with the use of evolutionary information.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2858251

26 November 2018

Protein contact prediction using patterns of correlation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2858251

26 November 2018

Prediction of beta-sheet topology and disulfide bridges in polypeptides.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2858251

26 November 2018

Ab initio prediction of helical segments in polypeptides.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2858251

26 November 2018

Prediction of contact maps with neural networks and correlated mutations.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2858251

26 November 2018

Improving contact predictions by the combination of correlated mutations and other sources of sequence information

1 reference

https://pubmed.ncbi.nlm.nih.gov/20225257

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Predicting interresidue contacts using templates and pathways

1 reference

https://pubmed.ncbi.nlm.nih.gov/20225257

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Specific recognition in the tertiary structure of beta-sheets of proteins

1 reference

https://pubmed.ncbi.nlm.nih.gov/20225257

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1002/PROT.22696

1 reference

Europe PubMed Central

PMC publication ID

17 September 2017

PMC publication ID

1 reference

Europe PubMed Central

PMC publication ID

17 September 2017

PubMed publication ID

1 reference

Europe PubMed Central

PMC publication ID

17 September 2017

ResearchGate publication ID

0 references

Sitelinks

Wikipedia(0 entries)

Wikibooks(0 entries)

Wikinews(0 entries)

Wikiquote(0 entries)

Wikisource(0 entries)

Wikiversity(0 entries)

Wikivoyage(0 entries)

Wiktionary(0 entries)

Multilingual sites(0 entries)

Retrieved from "https://www.wikidata.org/w/index.php?title=Q30386605&oldid=1549927080"