(Q34500105)

2 August 2017

title

PROSPER: an integrated feature-based tool for predicting protease substrate cleavage sites (English)

1 reference

2 August 2017

Andrew J Perry

3

0 references

Jiangning Song

Jiangning Song

1

0 references

Geoff Webb

Geoffrey I Webb

5

0 references

Robert N. Pike

Robert N Pike

7

0 references

James C Whisstock

James C Whisstock

6

0 references

Tatsuya Akutsu

4

Tatsuya Akutsu

1 reference

2 August 2017

Hao Tan

2

1 reference

2 August 2017

language of work or name

English

0 references

publication date

29 November 2012

1 reference

2 August 2017

1 reference

2 August 2017

volume

7

1 reference

2 August 2017

issue

11

1 reference

2 August 2017

page(s)

e50300

1 reference

Creative Commons Attribution 4.0 International

2 August 2017

copyright license

start time

29 November 2012

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

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7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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Structural and kinetic determinants of protease substrates

7 July 2018

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7 July 2018

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Proteome-wide substrate analysis indicates substrate exclusion as a mechanism to generate caspase-7 versus caspase-3 specificity

7 July 2018

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The crystal structure of caspase-6, a selective effector of axonal degeneration

7 July 2018

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Human caspases: activation, specificity, and regulation

7 July 2018

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7 July 2018

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Insights into the regulation of intrinsically disordered proteins in the human proteome by analyzing sequence and gene expression data.

7 July 2018

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Subsite cooperativity in protease specificity

7 July 2018

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Computational identification of protein methylation sites through bi-profile Bayes feature extraction

7 July 2018

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Detection of alpha-rod protein repeats using a neural network and application to huntingtin.

7 July 2018

1 reference

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M are better than one: an ensemble-based motif finder and its application to regulatory element prediction.

7 July 2018

1 reference

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

7 July 2018

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Allosteric regulation of proteases

7 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3510211

Protease substrate site predictors derived from machine learning on multilevel substrate phage display data

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3510211

PMAP: databases for analyzing proteolytic events and pathways

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3510211

Analysis of protein processing by N-terminal proteomics reveals novel species-specific substrate determinants of granzyme B orthologs

7 July 2018

1 reference

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Sequence based residue depth prediction using evolutionary information and predicted secondary structure

7 July 2018

1 reference

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The Degradome database: mammalian proteases and diseases of proteolysis

7 July 2018

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Global mapping of the topography and magnitude of proteolytic events in apoptosis

7 July 2018

1 reference

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7 July 2018

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Proteome-derived, database-searchable peptide libraries for identifying protease cleavage sites

7 July 2018

1 reference

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HSEpred: predict half-sphere exposure from protein sequences

7 July 2018

1 reference

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7 July 2018

1 reference

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Activated caspase-6 and caspase-6-cleaved fragments of huntingtin specifically colocalize in the nucleus

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3510211

Structural disorder serves as a weak signal for intracellular protein degradation.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3510211

PFRES: protein fold classification by using evolutionary information and predicted secondary structure.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3510211

Proteome-wide identification of family member-specific natural substrate repertoire of caspases

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3510211

Inferring function using patterns of native disorder in proteins

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3510211

Natively unstructured regions in proteins identified from contact predictions

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3510211

Natively unstructured loops differ from other loops

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3510211

Prediction of DNA-binding residues from sequence

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3510211

Protein-protein interaction hotspots carved into sequences

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3510211

Identification of proteolytic cleavage sites by quantitative proteomics

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3510211

SVM-based prediction of caspase substrate cleavage sites

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3510211

Intrinsic disorder and functional proteomics

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3510211

CutDB: a proteolytic event database

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3510211

Predicting residue-wise contact orders in proteins by support vector regression

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3510211

Targeting proteases: successes, failures and future prospects

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3510211

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3510211

Prediction of cis/trans isomerization in proteins using PSI-BLAST profiles and secondary structure information.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3510211

SCRATCH: a protein structure and structural feature prediction server

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3510211

GraBCas: a bioinformatics tool for score-based prediction of Caspase- and Granzyme B-cleavage sites in protein sequences

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3510211

Intrinsically unstructured proteins and their functions

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3510211

The International Protein Index: an integrated database for proteomics experiments

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3510211

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3510211

The importance of intrinsic disorder for protein phosphorylation

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3510211

Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3510211

A new method to estimate ligand-receptor energetics

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3510211

Protease degradomics: a new challenge for proteomics

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3510211

Caspase 3-cleaved N-terminal fragments of wild-type and mutant huntingtin are present in normal and Huntington's disease brains, associate with membranes, and undergo calpain-dependent proteolysis.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3510211

Gene ontology: tool for the unification of biology

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3510211

Caspase structure, proteolytic substrates, and function during apoptotic cell death

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3510211

Protein secondary structure prediction based on position-specific scoring matrices

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3510211

The caspase family of cysteine proteases

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3510211

Caspases: the executioners of apoptosis

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3510211

Site-specific dissection of substrate recognition by thrombin

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3510211

On the size of the active site in proteases. I. Papain

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3510211

Sequence logos: a new way to display consensus sequences

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3510211

Molecular recognition. Conformational analysis of limited proteolytic sites and serine proteinase protein inhibitors

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3510211

Comparison of the predicted and observed secondary structure of T4 phage lysozyme

7 July 2018

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3510211

7 July 2018

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0050300

Emerging roles of proteases in tumour suppression

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0050300

Proteome-wide analysis of protein carboxy termini: C terminomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0050300

Prediction of caspase cleavage sites using Bayesian bio-basis function neural networks.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0050300

CASVM: web server for SVM-based prediction of caspase substrates cleavage sites

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0050300

Protein Identification and Analysis Tools on the ExPASy Server

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0050300

CaSPredictor: a new computer-based tool for caspase substrate prediction.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0050300

PoPS: a computational tool for modeling and predicting protease specificity.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0050300

SitePredicting the cleavage of proteinase substrates.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0050300

Predicting disulfide connectivity from protein sequence using multiple sequence feature vectors and secondary structure.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0050300

DROP: an SVM domain linker predictor trained with optimal features selected by random forest

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0050300

The structural aspects of limited proteolysis of native proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0050300

The protein trinity--linking function and disorder.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0050300

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0050300

An ensemble framework for clustering protein-protein interaction networks.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0050300

Prediction of disordered regions in proteins based on the meta approach

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0050300

MEROPS: the peptidase database

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23209700

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PONE.0050300

1 reference

2 August 2017

0 references

1 reference

2 August 2017

1 reference