(Q30009321)

21 May 2017

title

Fast and accurate discovery of degenerate linear motifs in protein sequences (English)

1 reference

21 May 2017

Benjamin Dubreuil

2

0 references

Emmanuel D Levy

series ordinal

3

object named as

Emmanuel D Levy

1 reference

21 May 2017

4

Stephen W Michnick

1 reference

21 May 2017

Abdellali Kelil

1

1 reference

21 May 2017

language of work or name

English

0 references

publication date

10 September 2014

1 reference

21 May 2017

1 reference

21 May 2017

volume

9

1 reference

21 May 2017

issue

9

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21 May 2017

page(s)

e106081

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Creative Commons Attribution 4.0 International

21 May 2017

copyright license

start time

10 September 2014

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

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22 May 2017

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22 May 2017

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22 May 2017

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Computational design of high-affinity epitope scaffolds by backbone grafting of a linear epitope

22 May 2017

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Using the Basic Local Alignment Search Tool (BLAST)

22 May 2017

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ELM: the status of the 2010 eukaryotic linear motif resource

22 May 2017

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22 May 2017

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Structural, Functional, and Bioinformatic Studies Demonstrate the Crucial Role of an Extended Peptide Binding Site for the SH3 Domain of Yeast Abp1p

22 May 2017

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MEME SUITE: tools for motif discovery and searching

22 May 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160167

Function and structure of inherently disordered proteins

22 May 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160167

Short Linear Motifs recognized by SH2, SH3 and Ser/Thr Kinase domains are conserved in disordered protein regions

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160167

Recognition of non-canonical peptides by the yeast Fus1p SH3 domain: elucidation of a common mechanism for diverse SH3 domain specificities

22 May 2017

1 reference

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NestedMICA as an ab initio protein motif discovery tool

22 May 2017

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DILIMOT: discovery of linear motifs in proteins

22 May 2017

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Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences

22 May 2017

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IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160167

MUSCLE: multiple sequence alignment with high accuracy and high throughput

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160167

Prediction and Functional Analysis of Native Disorder in Proteins from the Three Kingdoms of Life

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160167

The importance of intrinsic disorder for protein phosphorylation

22 May 2017

1 reference

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Human protein reference database as a discovery resource for proteomics

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160167

GlobPlot: Exploring protein sequences for globularity and disorder

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160167

The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003

22 May 2017

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

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160167

Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160167

Detecting patterns in protein sequences

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160167

Fitting a mixture model by expectation maximization to discover motifs in biopolymers

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160167

Evaluating caveolin interactions: do proteins interact with the caveolin scaffolding domain through a widespread aromatic residue-rich motif?

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160167

Deciphering a global network of functionally associated post-translational modifications

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160167

Towards a theoretical understanding of false positives in DNA motif finding

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160167

Motif switches: decision-making in cell regulation

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160167

Proteome-wide discovery of evolutionary conserved sequences in disordered regions

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160167

The role of structural disorder in the rewiring of protein interactions through 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=4160167

Prediction of short linear protein binding regions

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160167

Attributes of short linear motifs.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160167

Bringing order to protein disorder through comparative genomics and genetic interactions

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160167

Large-scale discovery and characterization of protein regulatory motifs in eukaryotes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160167

How viruses hijack cell regulation

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160167

Computational identification and analysis of protein short linear motifs.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160167

Deciphering protein kinase specificity through large-scale analysis of yeast phosphorylation site motifs

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160167

The structural basis of peptide-protein binding strategies.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160167

ANCHOR: web server for predicting protein binding regions in disordered 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=4160167

ADAN: a database for prediction of protein-protein interaction of modular domains mediated by linear motifs

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160167

Structure-based prediction of the Saccharomyces cerevisiae SH3-ligand interactions

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160167

Tight regulation of unstructured proteins: from transcript synthesis to protein degradation

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160167

Approved drug mimics of short peptide ligands from protein interaction motifs

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160167

Understanding eukaryotic linear motifs and their role in cell signaling and regulation.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160167

SLiMFinder: a probabilistic method for identifying over-represented, convergently evolved, short linear motifs 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=4160167

Local structural disorder imparts plasticity on linear motifs.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160167

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160167

FoldIndex: a simple tool to predict whether a given protein sequence is intrinsically unfolded

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160167

Linear regression models for solvent accessibility prediction 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=4160167

The DISOPRED server for the prediction of protein disorder

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160167

SMART: identification and annotation of domains from signalling and extracellular protein sequences

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160167

Combinatorial pattern discovery in biological sequences: The TEIRESIAS algorithm.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160167

Apples to apples: improving the performance of motif finders and their significance analysis in the Twilight Zone.

3 June 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0106081

Masking residues using context-specific evolutionary conservation significantly improves short linear motif discovery

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0106081

Nested sampling for general Bayesian computation

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0106081

Weak functional constraints on phosphoproteomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0106081

Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0106081

Modeling peptide-protein interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0106081

10.1371/JOURNAL.PONE.0106081

21 January 2018

Identifiers

DOI

1 reference

21 May 2017

0 references

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