(Q30417356)

12 August 2017

Accurate de novo structure prediction of large transmembrane protein domains using fragment-assembly and correlated mutation analysis (English)

1 reference

protein structure prediction

12 August 2017

transmembrane protein

0 references

0 references

2

David T Jones

1 reference

12 August 2017

Timothy Nugent

1

1 reference

PMCID

3386101

12 August 2017

language of work or name

English

0 references

publication date

29 May 2012

1 reference

Proceedings of the National Academy of Sciences of the United States of America

12 August 2017

1 reference

12 August 2017

109

1 reference

12 August 2017

E1540-7

1 reference

12 August 2017

24

1 reference

Protein 3D structure computed from evolutionary sequence variation

12 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3386101

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3386101

Protein topology from predicted residue contacts

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3386101

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3386101

HMMER web server: interactive sequence similarity searching

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3386101

UniProt Knowledgebase: a hub of integrated protein data

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3386101

MEDELLER: homology-based coordinate generation for membrane 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=3386101

Predicting transmembrane helix packing arrangements using residue contacts and a force-directed algorithm

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3386101

How significant is a protein structure similarity with TM-score = 0.5?

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3386101

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3386101

The Pfam protein families database

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3386101

Parallel tempering: theory, applications, and new perspectives

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3386101

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3386101

Transmembrane protein topology prediction using support vector machines

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3386101

Biophysical dissection of membrane 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=3386101

Predicting helix-helix interactions from residue contacts in membrane 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=3386101

Prediction of membrane protein structures with complex topologies using limited constraints

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3386101

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3386101

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3386101

SPOCTOPUS: a combined predictor of signal peptides and membrane protein topology.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3386101

Prediction of membrane-protein topology from first principles

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3386101

Sparse inverse covariance estimation with the graphical lasso

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3386101

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3386101

Toward high-resolution prediction and design of transmembrane helical protein structures

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3386101

Towards genome-scale structure prediction for transmembrane 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=3386101

OPM: orientations of proteins in membranes database

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3386101

A study of the membrane-water interface region of membrane 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=3386101

Protein structure prediction using Rosetta

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3386101

The second extracellular loop of the dopamine D2 receptor lines the binding-site crevice

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3386101

Folding in lipid membranes (FILM): a novel method for the prediction of small membrane protein 3D structures

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3386101

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3386101

20 June 2018

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=3386101

Control of the selectivity of the aquaporin water channel family by global orientational tuning

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3386101

Comparative protein structure modeling of genes and genomes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3386101

Ab initio protein structure prediction of CASP III targets using ROSETTA

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3386101

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=3386101

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=3386101

How frequent are correlated changes in families of protein sequences?

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3386101

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3386101

A method for alpha-helical integral membrane protein fold 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=3386101

Prediction of helix-helix contacts and interacting helices in polytopic membrane proteins using neural networks

20 June 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1120036109

Effectiveness of correlation analysis in identifying protein residues undergoing correlated evolution.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1120036109

Reducing phylogenetic bias in correlated mutation analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1120036109

Mutual information without the influence of phylogeny or entropy dramatically improves residue contact prediction.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1120036109

Prediction of contact maps with neural networks and correlated mutations.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1120036109

Protein contact prediction using patterns of correlation

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1120036109

Using information theory to search for co-evolving residues in proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1120036109

ZPRED: predicting the distance to the membrane center for residues in alpha-helical membrane proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1120036109

Calculation of protein conformations by proton-proton distance constraints. A new efficient algorithm

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1120036109

Striped sheets and protein contact prediction

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1120036109

Assembling novel protein folds from super-secondary structural fragments

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1120036109

Successful ab initio prediction of the tertiary structure of NK-lysin using multiple sequences and recognized supersecondary structural motifs.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3386101

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/22645369

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1073/PNAS.1120036109

1 reference

12 August 2017

0 references

1 reference

12 August 2017

1 reference

PMCID

3386101