Predicting protein residue-residue contacts using deep networks and boosting (Q36432211)

14 August 2017

Predicting protein residue-residue contacts using deep networks and boosting (English)

1 reference

14 August 2017

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1

Jesse Eickholt

1 reference

14 August 2017

Jianlin Cheng

2

1 reference

PMC publication ID

3509494

14 August 2017

language of work or name

English

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publication date

9 October 2012

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14 August 2017

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14 August 2017

28

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14 August 2017

23

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14 August 2017

3066-3072

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Deep architectures for protein contact map prediction

14 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509494

PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509494

Predicting residue-residue contacts using random forest models

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509494

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509494

A conformation ensemble approach to protein residue-residue contact

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509494

Evaluation of residue-residue contact predictions in CASP9

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509494

Improving protein structure prediction using multiple sequence-based contact predictions

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509494

APOLLO: a quality assessment service for single and multiple protein models

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509494

Extending CATH: increasing coverage of the protein structure universe and linking structure with function

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509494

Predicted residue-residue contacts can help the scoring of 3D models

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509494

Assessment of domain boundary predictions and the prediction of intramolecular contacts in CASP8.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509494

Peptides modulating conformational changes in secreted chaperones: from in silico design to preclinical proof of concept

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509494

NNcon: improved protein contact map prediction using 2D-recursive neural networks

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509494

Using multi-data hidden Markov models trained on local neighborhoods of protein structure to predict residue-residue contacts

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509494

Ab initio and template-based prediction of multi-class distance maps by two-dimensional recursive neural networks

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509494

Using inferred residue contacts to distinguish between correct and incorrect protein models

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509494

Assessment of intramolecular contact predictions for CASP7.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509494

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509494

Reducing the dimensionality of data with neural networks

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509494

A fast learning algorithm for deep belief nets

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509494

CASP6 assessment of contact prediction.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509494

SCRATCH: a protein structure and structural feature prediction server

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509494

Solving the protein sequence metric problem

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509494

Training products of experts by minimizing contrastive divergence

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509494

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509494

30 September 2017

The Protein Data Bank

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509494

Sequence specificity, statistical potentials, and three-dimensional structure prediction with self-correcting distance geometry calculations of beta-sheet formation in proteins

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509494

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509494

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509494

Predicting residue-residue contact maps by a two-layer, integrated neural-network method

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509494

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

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509494

Prediction of protein beta-residue contacts by Markov logic networks with grounding-specific weights.

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509494

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

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509494

Protein contact prediction using patterns of correlation

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509494

Prediction of contact maps with neural networks and correlated mutations.

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509494

A Decision-Theoretic Generalization of On-Line Learning and an Application to Boosting

21 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093/BIOINFORMATICS/BTS598

Using a hydrophobic contact potential to evaluate native and near-native folds generated by molecular dynamics simulations

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23047561

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

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

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23047561

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

An empirical energy potential with a reference state for protein fold and sequence recognition

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23047561

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/BIOINFORMATICS/BTS598

1 reference

journals/bioinformatics/EickholtC12

14 August 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

PMC publication ID

3509494

14 August 2017

PubMed publication ID

23047561

1 reference

PMC publication ID

3509494