(Q62729918)

4

object named as

Tatsuya Akutsu

0 references

Kuo-Chen Chou

7

object named as

Kuo-Chen Chou

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author name string

Jiangning Song

1

0 references

Yanan Wang

2

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Fuyi Li

3

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Neil D Rawlings

Briefings in Bioinformatics

5

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language of work or name

English

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publication date

19 April 2018

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25 March 2019

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8 April 2021

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8 April 2021

Creative Commons Attribution 4.0 International

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Europe PubMed Central

Amino acid substitution matrices from protein blocks

8 April 2021

cites work

1 reference

12 December 2020

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

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12 December 2020

An alternate-subsite-coupled model for predicting HIV protease cleavage sites in proteins.

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12 December 2020

A vector projection approach to predicting HIV protease cleavage sites in proteins.

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12 December 2020

A vectorized sequence-coupling model for predicting HIV protease cleavage sites in proteins.

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12 December 2020

A formulation for correlating properties of peptides and its application to predicting human immunodeficiency virus protease-cleavable sites in proteins

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12 December 2020

Predicting human immunodeficiency virus protease cleavage sites in proteins by a discriminant function method

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12 December 2020

Prediction of human immunodeficiency virus protease cleavage sites in proteins

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12 December 2020

Neural network prediction of the HIV-1 protease cleavage sites.

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12 December 2020

Cleavage of the calpain inhibitor, calpastatin, during apoptosis

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12 December 2020

Protein secondary structure prediction based on position-specific scoring matrices

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12 December 2020

Gene ontology: tool for the unification of biology

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12 December 2020

Assessing the accuracy of prediction algorithms for classification: an overview

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12 December 2020

Prediction of protein cellular attributes using pseudo-amino acid composition

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12 December 2020

Using subsite coupling to predict signal peptides

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12 December 2020

How matrix metalloproteinases regulate cell behavior

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12 December 2020

Prediction of signal peptides using scaled window

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12 December 2020

Protease degradomics: a new challenge for proteomics

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12 December 2020

Regulation of cell death: the calcium-apoptosis link

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12 December 2020

Protein degradation and protection against misfolded or damaged proteins

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12 December 2020

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

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12 December 2020

Using amphiphilic pseudo amino acid composition to predict enzyme subfamily classes

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12 December 2020

Prediction of protein accessible surface areas by support vector regression

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12 December 2020

Prediction of protein B-factor profiles.

1 reference

12 December 2020

Linear regression models for solvent accessibility prediction in proteins.

1 reference

12 December 2020

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

1 reference

12 December 2020

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

1 reference

12 December 2020

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

1 reference

12 December 2020

Feature selection based on mutual information: criteria of max-dependency, max-relevance, and min-redundancy

1 reference

12 December 2020

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

1 reference

12 December 2020

1 reference

12 December 2020

The major human and mouse granzymes are structurally and functionally divergent

1 reference

12 December 2020

Prediction of linear B-cell epitopes using amino acid pair antigenicity scale.

1 reference

12 December 2020

SVM-based prediction of caspase substrate cleavage sites

1 reference

12 December 2020

Inhibitor design for SARS coronavirus main protease based on "distorted key theory".

1 reference

12 December 2020

Prediction of flexible/rigid regions from protein sequences using k-spaced amino acid pairs

1 reference

12 December 2020

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

1 reference

12 December 2020

Inferring function using patterns of native disorder in proteins

1 reference

12 December 2020

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

1 reference

12 December 2020

AAindex: amino acid index database, progress report 2008

1 reference

12 December 2020

HIVcleave: a web-server for predicting human immunodeficiency virus protease cleavage sites in proteins

1 reference

12 December 2020

Prediction of protein structural class using novel evolutionary collocation-based sequence representation.

1 reference

12 December 2020

HSEpred: predict half-sphere exposure from protein sequences

1 reference

12 December 2020

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

1 reference

12 December 2020

Prediction of integral membrane protein type by collocated hydrophobic amino acid pairs

1 reference

12 December 2020

ProtIdent: a web server for identifying proteases and their types by fusing functional domain and sequential evolution information

1 reference

12 December 2020

Identification of proteases and their types

1 reference

12 December 2020

Allosteric regulation of proteases

1 reference

12 December 2020

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

1 reference

12 December 2020

SitePredicting the cleavage of proteinase substrates.

1 reference

12 December 2020

Methods for the proteomic identification of protease substrates

1 reference

12 December 2020

Prodepth: predict residue depth by support vector regression approach from protein sequences only

1 reference

12 December 2020

Structural and kinetic determinants of protease substrates

1 reference

12 December 2020

A multi-factor model for caspase degradome prediction

1 reference

12 December 2020

Cascleave: towards more accurate prediction of caspase substrate cleavage sites

1 reference

12 December 2020

Prediction of protease substrates using sequence and structure features

1 reference

12 December 2020

Pripper: prediction of caspase cleavage sites from whole proteomes

1 reference

12 December 2020

Musite, a tool for global prediction of general and kinase-specific phosphorylation sites.

1 reference

12 December 2020

Some remarks on protein attribute prediction and pseudo amino acid composition

1 reference

12 December 2020

Bioinformatic approaches for predicting substrates of proteases

1 reference

12 December 2020

Redesigning allosteric activation in an enzyme

1 reference

12 December 2020

GPS-CCD: a novel computational program for the prediction of calpain cleavage sites

1 reference

12 December 2020

Calpain cleavage prediction using multiple kernel learning.

1 reference

12 December 2020

Structural determinants of limited proteolysis

1 reference

12 December 2020

Identifying and quantifying proteolytic events and the natural N terminome by terminal amine isotopic labeling of substrates

1 reference

12 December 2020

A review of statistical methods for prediction of proteolytic cleavage

1 reference

12 December 2020

Developing a powerful in silico tool for the discovery of novel caspase-3 substrates: a preliminary screening of the human proteome.

1 reference

12 December 2020

TANGLE: two-level support vector regression approach for protein backbone torsion angle prediction from primary sequences

1 reference

12 December 2020

Protease signalling: the cutting edge

1 reference

12 December 2020

FunSAV: predicting the functional effect of single amino acid variants using a two-stage random forest model

1 reference

12 December 2020

CD-HIT: accelerated for clustering the next-generation sequencing data

1 reference

12 December 2020

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

1 reference

12 December 2020

iRSpot-PseDNC: identify recombination spots with pseudo dinucleotide composition

1 reference

12 December 2020

iSNO-PseAAC: predict cysteine S-nitrosylation sites in proteins by incorporating position specific amino acid propensity into pseudo amino acid composition

1 reference

12 December 2020

Some remarks on predicting multi-label attributes in molecular biosystems

1 reference

12 December 2020

hCKSAAP_UbSite: improved prediction of human ubiquitination sites by exploiting amino acid pattern and properties

1 reference

12 December 2020

Incorporating key position and amino acid residue features to identify general and species-specific Ubiquitin conjugation sites.

1 reference

12 December 2020

pLogo: a probabilistic approach to visualizing sequence motifs.

1 reference

12 December 2020

iSNO-AAPair: incorporating amino acid pairwise coupling into PseAAC for predicting cysteine S-nitrosylation sites in proteins

1 reference

12 December 2020

Cascleave 2.0, a new approach for predicting caspase and granzyme cleavage targets.

1 reference

12 December 2020

PseKNC: a flexible web server for generating pseudo K-tuple nucleotide composition.

1 reference

12 December 2020

iHyd-PseAAC: predicting hydroxyproline and hydroxylysine in proteins by incorporating dipeptide position-specific propensity into pseudo amino acid composition

1 reference

12 December 2020

Network analyses reveal pervasive functional regulation between proteases in the human protease web

1 reference

12 December 2020

iNitro-Tyr: prediction of nitrotyrosine sites in proteins with general pseudo amino acid composition

1 reference

12 December 2020

Towards more accurate prediction of ubiquitination sites: a comprehensive review of current methods, tools and features

1 reference

12 December 2020

PseKNC-General: a cross-platform package for generating various modes of pseudo nucleotide compositions

1 reference

12 December 2020

UniProt: a hub for protein information

1 reference

12 December 2020

iPro54-PseKNC: a sequence-based predictor for identifying sigma-54 promoters in prokaryote with pseudo k-tuple nucleotide composition

1 reference

12 December 2020

Pericellular proteolysis in cancer

1 reference

12 December 2020

Prediction of β-lactamase and its class by Chou's pseudo-amino acid composition and support vector machine

1 reference

12 December 2020

repDNA: a Python package to generate various modes of feature vectors for DNA sequences by incorporating user-defined physicochemical properties and sequence-order effects

1 reference

12 December 2020

Impacts of bioinformatics to medicinal chemistry

1 reference

12 December 2020

GlycoMine: a machine learning-based approach for predicting N-, C- and O-linked glycosylation in the human proteome

1 reference

12 December 2020

Pse-in-One: a web server for generating various modes of pseudo components of DNA, RNA, and protein sequences

1 reference

12 December 2020

CleavPredict: A Platform for Reasoning about Matrix Metalloproteinases Proteolytic Events

1 reference

12 December 2020

1 reference

12 December 2020

repRNA: a web server for generating various feature vectors of RNA sequences.

1 reference

12 December 2020

Pseudo nucleotide composition or PseKNC: an effective formulation for analyzing genomic sequences

1 reference

12 December 2020

Twenty years of the MEROPS database of proteolytic enzymes, their substrates and inhibitors.

1 reference

12 December 2020

Prediction of Protein Submitochondrial Locations by Incorporating Dipeptide Composition into Chou's General Pseudo Amino Acid Composition

1 reference

12 December 2020

pSuc-Lys: Predict lysine succinylation sites in proteins with PseAAC and ensemble random forest approach.

1 reference

12 December 2020

Periscope: quantitative prediction of soluble protein expression in the periplasm of Escherichia coli

1 reference

12 December 2020

iACP: a sequence-based tool for identifying anticancer peptides

1 reference

12 December 2020

iRSpot-EL: identify recombination spots with an ensemble learning approach

1 reference

12 December 2020

Analysis and comparison of lignin peroxidases between fungi and bacteria using three different modes of Chou's general pseudo amino acid composition

1 reference

12 December 2020

iOri-Human: identify human origin of replication by incorporating dinucleotide physicochemical properties into pseudo nucleotide composition

1 reference

12 December 2020

GlycoMine(struct): a new bioinformatics tool for highly accurate mapping of the human N-linked and O-linked glycoproteomes by incorporating structural features

1 reference

12 December 2020

iRNA-AI: identifying the adenosine to inosine editing sites in RNA sequences.

1 reference

12 December 2020

Unb-DPC: Identify mycobacterial membrane protein types by incorporating un-biased dipeptide composition into Chou's general PseAAC.

1 reference

12 December 2020

Pse-Analysis: a python package for DNA/RNA and protein/ peptide sequence analysis based on pseudo components and kernel methods

1 reference

12 December 2020

Prediction of HIV-1 protease cleavage site using a combination of sequence, structural, and physicochemical features

1 reference

12 December 2020

Predicting antimicrobial peptides with improved accuracy by incorporating the compositional, physico-chemical and structural features into Chou's general PseAAC.

1 reference

12 December 2020

An Unprecedented Revolution in Medicinal Chemistry Driven by the Progress of Biological Science

1 reference

12 December 2020

iPreny-PseAAC: identify C-terminal cysteine prenylation sites in proteins by incorporating two tiers of sequence couplings into PseAAC.

1 reference

12 December 2020

iRNA-PseColl: Identifying the Occurrence Sites of Different RNA Modifications by Incorporating Collective Effects of Nucleotides into PseKNC.

1 reference

12 December 2020

2L-piRNA: A Two-Layer Ensemble Classifier for Identifying Piwi-Interacting RNAs and Their Function

1 reference

12 December 2020

pLoc-mPlant: predict subcellular localization of multi-location plant proteins by incorporating the optimal GO information into general PseAAC.

1 reference

12 December 2020

Knowledge-transfer learning for prediction of matrix metalloprotease substrate-cleavage sites

1 reference

12 December 2020

pLoc-mVirus: Predict subcellular localization of multi-location virus proteins via incorporating the optimal GO information into general PseAAC.

1 reference

12 December 2020

PhosphoPredict: A bioinformatics tool for prediction of human kinase-specific phosphorylation substrates and sites by integrating heterogeneous feature selection

1 reference

12 December 2020

iPromoter-2L: a two-layer predictor for identifying promoters and their types by multi-window-based PseKNC.

1 reference

12 December 2020

pLoc-mAnimal: predict subcellular localization of animal proteins with both single and multiple sites

1 reference

12 December 2020

PROSPERous: high-throughput prediction of substrate cleavage sites for 90 proteases with improved accuracy.

1 reference

12 December 2020

Prediction of protein subcellular localization with oversampling approach and Chou's general PseAAC.

1 reference

12 December 2020

B-factor profile prediction for RNA flexibility using support vector machines.

1 reference

12 December 2020

BioSeq-Analysis: a platform for DNA, RNA and protein sequence analysis based on machine learning approaches

1 reference

12 December 2020

A Novel Modeling in Mathematical Biology for Classification of Signal Peptides

1 reference

12 December 2020

iDNA6mA-PseKNC: Identifying DNA N6-methyladenosine sites by incorporating nucleotide physicochemical properties into PseKNC.

1 reference

12 December 2020

iFeature: a python package and web server for features extraction and selection from protein and peptide sequences.

1 reference

12 December 2020

journals/bib/SongWLARWC19

Identifiers

DOI

10.1093/BIB/BBY028

0 references

DBLP publication ID

1 reference