Bringing order to protein disorder through comparative genomics and genetic interactions (Q30399739)

5 September 2017

Bringing order to protein disorder through comparative genomics and genetic interactions (English)

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5 September 2017

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8

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5 September 2017

Magali Michaut

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author name string

Jeremy Bellay

1

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5 September 2017

Sangjo Han

2

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5 September 2017

Taehyung Kim

4

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5 September 2017

Michael Costanzo

5

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5 September 2017

Brenda J Andrews

6

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5 September 2017

Charles Boone

7

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5 September 2017

Chad L Myers

9

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5 September 2017

Philip M Kim

10

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5 September 2017

16 February 2011

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5 September 2017

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5 September 2017

12

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5 September 2017

2

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5 September 2017

R14

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describes a project that uses

5 September 2017

Cytoscape

object named as

Cytoscape

2 references

9 June 2022

https://europepmc.org/search?query=(METHODS:'Cytoscape')

based on heuristic

inferred from PubMed Central ID database lookup

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

cites work

Molecular simulations of protein disorder

1 reference

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Intrinsically disordered chaperones in plants and animals.

14 July 2018

1 reference

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Pathway analysis of dilated cardiomyopathy using global proteomic profiling and enrichment maps

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188796

The genetic landscape of a cell

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188796

Protein secondary structure appears to be robust under in silico evolution while protein disorder appears not to be.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188796

Evolution of phosphoregulation: comparison of phosphorylation patterns across yeast species

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188796

Integrated assessment of genomic correlates of protein evolutionary rate

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188796

Linking folding and binding

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188796

Jalview Version 2--a multiple sequence alignment editor and analysis workbench

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188796

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188796

Network hubs buffer environmental variation in Saccharomyces cerevisiae

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188796

The unfoldomics decade: an update on intrinsically disordered proteins.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188796

High-quality binary protein interaction map of the yeast interactome network

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188796

The chemical genomic portrait of yeast: uncovering a phenotype for all genes

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188796

A multidimensional chromatography technology for in-depth phosphoproteome analysis

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188796

A sliding docking interaction is essential for sequential and processive phosphorylation of an SR protein by SRPK1

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188796

PAML 4: phylogenetic analysis by maximum likelihood

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188796

Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188796

Relating three-dimensional structures to protein networks provides evolutionary insights

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188796

Intrinsic disorder and functional proteomics

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188796

A scalable method for integration and functional analysis of multiple microarray datasets

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188796

Finding function: evaluation methods for functional genomic data

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188796

Alternative splicing in concert with protein intrinsic disorder enables increased functional diversity in multicellular organisms

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188796

Conservation of intrinsic disorder in protein domains and families: II. functions of conserved disorder

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188796

Conservation of intrinsic disorder in protein domains and families: I. A database of conserved predicted disordered regions

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188796

Global landscape of protein complexes in the yeast Saccharomyces cerevisiae

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188796

Proteome survey reveals modularity of the yeast cell machinery

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188796

The interplay between structure and function in intrinsically unstructured proteins.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188796

Intrinsically unstructured proteins and their functions

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188796

MAFFT version 5: improvement in accuracy of multiple sequence alignment

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188796

MUSCLE: a multiple sequence alignment method with reduced time and space complexity

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188796

The role of structural disorder in the function of RNA and protein chaperones

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188796

Evidence for dynamically organized modularity in the yeast protein-protein interaction network

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188796

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188796

The importance of intrinsic disorder for protein phosphorylation

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188796

Protein disorder prediction: implications for structural proteomics

14 July 2018

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188796

14 July 2018

https://api.crossref.org/works/10.1186%2FGB-2011-12-2-R14

Cytoscape: a software environment for integrated models of biomolecular interaction networks

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188796

Mutual induced fit binding of Xenopus ribosomal protein L5 to 5S rRNA.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188796

Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188796

Activation of the Bur1-Bur2 cyclin-dependent kinase complex by Cak1.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188796

Precision and functional specificity in mRNA decay

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188796

Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188796

Dissecting the regulatory circuitry of a eukaryotic genome

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188796

Intrinsic protein disorder and interaction promiscuity are widely associated with dosage sensitivity.

14 July 2018

1 reference

https://api.crossref.org/works/10.1186%2FGB-2011-12-2-R14

Flavors of protein disorder

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FGB-2011-12-2-R14

Evolution of characterized phosphorylation sites in budding yeast.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FGB-2011-12-2-R14

Dissection of the ATP-induced conformational cycle of the molecular chaperone Hsp90.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FGB-2011-12-2-R14

Hydrophilic residues 526 KNDAAD 531 in the flexible C-terminal region of the chaperonin GroEL are critical for substrate protein folding within the central cavity.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FGB-2011-12-2-R14

Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FGB-2011-12-2-R14

Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FGB-2011-12-2-R14

The role of disorder in interaction networks: a structural analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FGB-2011-12-2-R14

Assessment of disorder predictions in CASP8

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FGB-2011-12-2-R14

21 January 2018

Identifiers

DOI

10.1186/GB-2011-12-2-R14

1 reference

5 September 2017

1 reference

5 September 2017

PubMed publication ID

21324131

1 reference