(Q34496256)

2 August 2017

Direct-Coupling Analysis of nucleotide coevolution facilitates RNA secondary and tertiary structure prediction (English)

1 reference

2 August 2017

0 references

1 reference

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26420827%20AND%20SRC:MED&resulttype=core&format=json

3 June 2020

Simona Cocco

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26420827%20AND%20SRC:MED&resulttype=core&format=json

3 June 2020

author name string

Eleonora De Leonardis

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26420827%20AND%20SRC:MED&resulttype=core&format=json

3 June 2020

Benjamin Lutz

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26420827%20AND%20SRC:MED&resulttype=core&format=json

3 June 2020

Sebastian Ratz

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26420827%20AND%20SRC:MED&resulttype=core&format=json

3 June 2020

Rémi Monasson

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26420827%20AND%20SRC:MED&resulttype=core&format=json

3 June 2020

Alexander Schug

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26420827%20AND%20SRC:MED&resulttype=core&format=json

3 June 2020

language of work or name

English

0 references

publication date

29 September 2015

1 reference

2 August 2017

Nucleic Acids Research

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26420827%20AND%20SRC:MED&resulttype=core&format=json

3 June 2020

volume

43

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26420827%20AND%20SRC:MED&resulttype=core&format=json

3 June 2020

issue

21

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26420827%20AND%20SRC:MED&resulttype=core&format=json

3 June 2020

page(s)

10444-10455

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26420827%20AND%20SRC:MED&resulttype=core&format=json

Creative Commons Attribution 4.0 International

3 June 2020

copyright license

start time

11 November 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures

1 reference

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RNA-mediated epigenetic regulation of gene expression

6 July 2018

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MetaPSICOV: combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins.

6 July 2018

1 reference

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Rfam 12.0: updates to the RNA families database

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666395

Improved contact predictions using the recognition of protein like contact patterns

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666395

Sequence co-evolution gives 3D contacts and structures of protein complexes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666395

Robust and accurate prediction of residue-residue interactions across protein interfaces using evolutionary information.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666395

Computational modeling of RNA 3D structures, with the aid of experimental restraints

6 July 2018

1 reference

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The rise of regulatory RNA

6 July 2018

1 reference

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Standardization of RNA chemical mapping experiments

6 July 2018

1 reference

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Structure determination of noncanonical RNA motifs guided by ¹H NMR chemical shifts

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666395

Long non-coding RNAs: new players in cell differentiation and development

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666395

Differences between cotranscriptional and free riboswitch folding

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666395

Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666395

Infernal 1.1: 100-fold faster RNA homology searches

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666395

Emerging methods in protein co-evolution

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666395

RNA interference in the nucleus: roles for small RNAs in transcription, epigenetics and beyond

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666395

Structural constraints identified with covariation analysis in ribosomal RNA

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666395

Genomics-aided structure prediction

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666395

Structural basis of histidine kinase autophosphorylation deduced by integrating genomics, molecular dynamics, and mutagenesis

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666395

Three-dimensional structures of membrane proteins from genomic sequencing

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666395

Cooperative tertiary interaction network guides RNA folding.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666395

RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666395

Protein 3D structure computed from evolutionary sequence variation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666395

A two-dimensional mutate-and-map strategy for non-coding RNA structure

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666395

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666395

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666395

Non-coding RNAs in human disease

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666395

Computational approaches to 3D modeling of RNA.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666395

ModeRNA: a tool for comparative modeling of RNA 3D structure

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666395

Assemble: an interactive graphical tool to analyze and build RNA architectures at the 2D and 3D levels

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666395

Robust and generic RNA modeling using inferred constraints: a structure for the hepatitis C virus IRES pseudoknot domain

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666395

Atomic accuracy in predicting and designing noncanonical RNA structure

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666395

High-resolution protein complexes from integrating genomic information with molecular simulation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666395

Nonlocal helix formation is key to understanding S-adenosylmethionine-1 riboswitch function

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666395

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666395

RNAalifold: improved consensus structure prediction for RNA alignments

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666395

Macromolecular modeling with rosetta

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666395

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666395

The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666395

Structure of the S-adenosylmethionine riboswitch regulatory mRNA element

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666395

Rfam: annotating non-coding RNAs in complete genomes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666395

Vienna RNA secondary structure server

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666395

The non-Watson-Crick base pairs and their associated isostericity matrices

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666395

6 July 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=4666395

The Ribonuclease P Database

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666395

RNA sequence analysis using covariance models

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666395

Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666395

Fast algorithm for predicting the secondary structure of single-stranded RNA

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666395

Inferring consensus structure from nucleic acid sequences.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666395

Identifying constraints on the higher-order structure of RNA: continued development and application of comparative sequence analysis methods

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666395

Inferring consensus structure from nucleic acid sequences

6 July 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FNAR%2FGKV932

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

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FNAR%2FGKV932

Base Pairing Constraints Drive Structural Epistasis in Ribosomal RNA Sequences

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FNAR%2FGKV932

21 January 2018

Identifiers

DOI

10.1093/NAR/GKV932

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26420827%20AND%20SRC:MED&resulttype=core&format=json

3 June 2020

1 reference

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26420827%20AND%20SRC:MED&resulttype=core&format=json

3 June 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26420827%20AND%20SRC:MED&resulttype=core&format=json