Evaluation of residue-residue contact prediction in CASP10 (Q29048194)

5

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Daniel D'Andrea

2

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Bohdan Monastyrskyy

1

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Anna Tramontano

4

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Krzysztof Fidelis

Protein structure prediction from sequence variation

3

object named as

Krzysztof Fidelis

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language of work or name

English

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publication date

February 2014

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published in

Proteins

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volume

82 Suppl 2

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page(s)

138-53

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cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823628

Protein 3D structure computed from evolutionary sequence variation

6 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823628

Direct-coupling analysis of residue coevolution captures native contacts across many protein families

6 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823628

Evaluation of disorder predictions in CASP9

6 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823628

Evaluation of residue-residue contact predictions in CASP9

6 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823628

Disentangling direct from indirect co-evolution of residues in protein alignments

6 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823628

Structural principles of leucine-rich repeat (LRR) proteins

6 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823628

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

6 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823628

6 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823628

Identification of direct residue contacts in protein-protein interaction by message passing

6 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823628

Definition and classification of evaluation units for CASP10

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823628

CASP prediction center infrastructure and evaluation measures in CASP10 and CASP ROLL.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823628

Emerging methods in protein co-evolution

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823628

Deep architectures for protein contact map 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=3823628

Genomics-aided structure 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=3823628

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823628

Predicting residue-residue contacts using random forest 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=3823628

Improving protein structure prediction using multiple sequence-based contact predictions

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823628

Effects of site-directed mutagenesis of mglA on motility and swarming of Myxococcus xanthus

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823628

MULTICOM: a multi-level combination approach to protein structure prediction and its assessments in CASP8

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823628

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823628

SAM-T08, HMM-based protein structure 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=3823628

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823628

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823628

Predicting key long-range interaction sites by B-factors

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823628

A comprehensive assessment of sequence-based and template-based methods for protein contact 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=3823628

Assessment of intramolecular contact predictions for CASP7.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823628

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823628

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823628

Physically realistic homology models built with ROSETTA can be more accurate than their templates

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823628

CASP6 assessment of contact 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=3823628

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823628

Analysis of mammalian cytochrome P450 structure and function by site-directed mutagenesis

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823628

A neural network based predictor of residue contacts in 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=3823628

Recovery of protein structure from contact maps

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823628

A geometrical constraint approach for reproducing the native backbone conformation of a protein.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823628

Protein fold refinement: building models from idealized folds using motif constraints and multiple sequence data

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823628

Can three-dimensional contacts in protein structures be predicted by analysis of correlated mutations?

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823628

Three-dimensional structure of proteins determined by molecular dynamics with interproton distance restraints: application to crambin

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823628

A comparison of the restrained molecular dynamics and distance geometry methods for determining three-dimensional structures of proteins on the basis of interproton distances

3 June 2018

1 reference

Protein structures from distance inequalities.

21 January 2018

1 reference

MONSSTER: a method for folding globular proteins with a small number of distance restraints

21 January 2018

1 reference

FT-COMAR: fault tolerant three-dimensional structure reconstruction from protein contact maps

21 January 2018

1 reference

Contact prediction using mutual information and neural nets

21 January 2018

1 reference

Prediction of contact maps with neural networks and correlated mutations.

21 January 2018

1 reference

Probing electrostatic interactions and ligand binding in aspartyl-tRNA synthetase through site-directed mutagenesis and computer simulations

21 January 2018

1 reference

Challenging the state of the art in protein structure prediction: Highlights of experimental target structures for the 10th Critical Assessment of Techniques for Protein Structure Prediction Experiment CASP10

21 January 2018

1 reference

CASP10 results compared to those of previous CASP experiments

21 January 2018

1 reference

21 January 2018

Distance between Sets

1 reference

A Response to Webb and Ting?s On the Application of ROC Analysis to Predict Classification Performance Under Varying Class Distributions

21 January 2018

1 reference

Predicting contact map using radial basis function neural network with conformational energy function

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823628

Comparative experiments on learning information extractors for proteins and their interactions.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823628

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

26 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23760879

12 December 2020

inferred from PubMed ID database lookup

CASP2: report on ab initio predictions

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23760879

12 December 2020

inferred from PubMed ID database lookup

Effector recognition by the small GTP-binding proteins Ras and Ral

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23760879

12 December 2020

inferred from PubMed ID database lookup

Identifiers

DOI

10.1002/PROT.24340

0 references

Fatcat ID

release_l7ib3ulw5vdj5alad26fcnubpm

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/l7ib3ulw5vdj5alad26fcnubpm

24 November 2022