\textbf{iLoc-Virus}: a multi-label learning classifier for identifying the subcellular localization of virus proteins with both single and multiple sites

DOI10.1016/j.jtbi.2011.06.005zbMath1397.92238OpenAlexW2010211703WikidataQ38501790 ScholiaQ38501790MaRDI QIDQ1786031

Kuo-Chen Chou, Zhi-Cheng Wu, Xuan Xiao

Publication date: 24 September 2018

Published in: Journal of Theoretical Biology (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.1016/j.jtbi.2011.06.005

zbMATH Keywords

absolute accuracyaccumulation-layer scalelocative proteinsML-KNNmultiplex proteins

Mathematics Subject Classification ID

Learning and adaptive systems in artificial intelligence (68T05) Biochemistry, molecular biology (92C40) Cell biology (92C37) Computational methods for problems pertaining to biology (92-08)

Related Items (35)

Predicting plant protein subcellular multi-localization by Chou's PseAAC formulation based multi-label homolog knowledge transfer learning ⋮ Annotating the protein-RNA interaction sites in proteins using evolutionary information and protein backbone structure ⋮ Comprehensive comparative analysis and identification of RNA-binding protein domains: multi-class classification and feature selection ⋮ VR-BFDT: a variance reduction based binary fuzzy decision tree induction method for protein function prediction ⋮ Predicting Golgi-resident protein types using pseudo amino acid compositions: approaches with positional specific physicochemical properties ⋮ pSuc-Lys: predict lysine succinylation sites in proteins with PseAAC and ensemble random forest approach ⋮ Predicting Gram-positive bacterial protein subcellular localization based on localization motifs ⋮ iCDI-PseFpt: identify the channel-drug interaction in cellular networking with PseAAC and molecular fingerprints ⋮ Protein subcellular localization in human and hamster cell lines: employing local ternary patterns of fluorescence microscopy images ⋮ \textit{SVM} ensemble based transfer learning for large-scale membrane proteins discrimination ⋮ Robust feature generation for protein subchloroplast location prediction with a weighted GO transfer model ⋮ Naïve Bayes classifier with feature selection to identify phage virion proteins ⋮ Gram-positive and Gram-negative protein subcellular localization by incorporating evolutionary-based descriptors into Chou's general PseAAC ⋮ Protein fold recognition by alignment of amino acid residues using kernelized dynamic time warping ⋮ Human proteins characterization with subcellular localizations ⋮ Prediction of antioxidant proteins by incorporating statistical moments based features into Chou's PseAAC ⋮ Characterization of structure-antioxidant activity relationship of peptides in free radical systems using QSAR models: key sequence positions and their amino acid properties ⋮ QSAR prediction of HIV-1 protease inhibitory activities using docking derived molecular descriptors ⋮ Identification of protein subcellular localization via integrating evolutionary and physicochemical information into Chou's general PseAAC ⋮ Predicting protein-protein interactions by fusing various Chou's pseudo components and using wavelet denoising approach ⋮ SPrenylC-PseAAC: a sequence-based model developed via Chou's 5-steps rule and general PseAAC for identifying S-prenylation sites in proteins ⋮ iPHLoc-ES: identification of bacteriophage protein locations using evolutionary and structural features ⋮ Prediction of protein subcellular localization with oversampling approach and Chou's general PseAAC ⋮ Sequence-dependent prediction of recombination hotspots in \textit{Saccharomyces cerevisiae} ⋮ A new hybrid fractal algorithm for predicting thermophilic nucleotide sequences ⋮ Multi-kernel transfer learning based on Chou's PseAAC formulation for protein submitochondria localization ⋮ Prediction of protein-protein interaction sites using patch-based residue characterization ⋮ Predicting mycobacterial proteins subcellular locations by incorporating pseudo-average chemical shift into the general form of Chou's pseudo amino acid composition ⋮ RFCRYS: sequence-based protein crystallization propensity prediction by means of random forest ⋮ Predicting protein subchloroplast locations with both single and multiple sites via three different modes of Chou's pseudo amino acid compositions ⋮ Prediction of Golgi-resident protein types using general form of Chou's pseudo-amino acid compositions: approaches with minimal redundancy maximal relevance feature selection ⋮ mLASSO-Hum: a LASSO-based interpretable human-protein subcellular localization predictor ⋮ R3P-Loc: a compact multi-label predictor using ridge regression and random projection for protein subcellular localization ⋮ iLoc-Virus ⋮ GOASVM: a subcellular location predictor by incorporating term-frequency gene ontology into the general form of Chou's pseudo-amino acid composition

Uses Software

• Cell-PLoc
• Psortb
• ProtIdent
• GPCR-2L
• Virus-ploc
• SubChlo
• Plant-mPLoc
• Quat-2L
• SecretP
• QuatIdent
• Gneg-mPLoc
• Euk-mPLoc

Cites Work

• Unnamed Item
• Predicting protein fold pattern with functional domain and sequential evolution information
• Use of fuzzy clustering technique and matrices to classify amino acids and its impact to Chou's pseudo amino acid composition
• Using the augmented Chou's pseudo amino acid composition for predicting protein submitochondria locations based on auto covariance approach
• \(\gamma\)-turn types prediction in proteins using the two-stage hybrid neural discriminant model
• SubChlo: predicting protein subchloroplast locations with pseudo-amino acid composition and the evidence-theoretic \(K\)-nearest neighbor (ET-KNN) algorithm
• A novel feature representation method based on Chou's pseudo amino acid composition for protein structural class prediction
• Predicting membrane protein types by fusing composite protein sequence features into pseudo amino acid composition
• Some remarks on protein attribute prediction and pseudo amino acid composition
• Using the concept of Chou's pseudo amino acid composition for risk type prediction of human papillomaviruses
• Gneg-mPLoc: a top-down strategy to enhance the quality of predicting subcellular localization of Gram-negative bacterial proteins
• SecretP: identifying bacterial secreted proteins by fusing new features into Chou's pseudo-amino acid composition
• The modified Mahalanobis discriminant for predicting outer membrane proteins by using Chou's pseudo amino acid composition
• Pseudo amino acid composition and multi-class support vector machines approach for conotoxin superfamily classification
• Prediction of apoptosis protein subcellular location using improved hybrid approach and pseudo-amino acid composition
• Using Chou's amphiphilic pseudo-amino acid composition and support vector machine for prediction of enzyme subfamily classes
• Predicting ion channels and their types by the dipeptide mode of pseudo amino acid composition
• Statistics of local complexity in amino acid sequences and sequence databases

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