Some remarks on protein attribute prediction and pseudo amino acid composition

From MaRDI portal

Publication:1670702

Jump to:navigation, search

DOI10.1016/j.jtbi.2010.12.024zbMath1405.92212OpenAlexW2034070267WikidataQ37822128 ScholiaQ37822128MaRDI QIDQ1670702

Kuo-Chen Chou

Publication date: 6 September 2018

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

Full work available at URL: http://europepmc.org/articles/pmc7125570

zbMATH Keywords

cross-validation PseAAC functional domain mode gene ontology mode sequential evolution mode

Mathematics Subject Classification ID

Protein sequences, DNA sequences (92D20) Research exposition (monographs, survey articles) pertaining to biology (92-02)

Related Items

Alignment free comparison: similarity distribution between the DNA primary sequences based on the shortest absent word, Predicting plant protein subcellular multi-localization by Chou's PseAAC formulation based multi-label homolog knowledge transfer learning, A method to distinguish between lysine acetylation and lysine methylation from protein sequences, Elman RNN based classification of proteins sequences on account of their mutual information, 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, 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, RBSURFpred: modeling protein accessible surface area in real and binary space using regularized and optimized regression, An estimator for local analysis of genome based on the minimal absent word, Comparison of genomic data via statistical distribution, NucPosPred: predicting species-specific genomic nucleosome positioning via four different modes of general PseKNC, Predicting protein submitochondrial locations by incorporating the pseudo-position specific scoring matrix into the general Chou's pseudo-amino acid composition, Identifying 5-methylcytosine sites in RNA sequence using composite encoding feature into Chou's PseKNC, IMem-2LSAAC: a two-level model for discrimination of membrane proteins and their types by extending the notion of SAAC into Chou's pseudo amino acid composition, Sequence-based discrimination of protein-RNA interacting residues using a probabilistic approach, Classify vertebrate hemoglobin proteins by incorporating the evolutionary information into the general PseAAC with the hybrid approach, Characterization of BioPlex network by topological properties, Precision assessment of some supervised and unsupervised algorithms for genotype discrimination in the genus \textit{pisum} using SSR molecular data, Naïve Bayes classifier with feature selection to identify phage virion proteins, Using temperature effects to predict the interactions between two RNAs, Gram-positive and Gram-negative protein subcellular localization by incorporating evolutionary-based descriptors into Chou's general PseAAC, Distribution bias of the sequence matching between exons and introns in exon joint and EJC binding region in \textit{C. elegans}, PSSM-Suc: accurately predicting succinylation using position specific scoring matrix into bigram for feature extraction, Prediction of metastasis in advanced colorectal carcinomas using CGH data, Prediction of S-sulfenylation sites using mRMR feature selection and fuzzy support vector machine algorithm, BlaPred: predicting and classifying \(\beta\)-lactamase using a 3-tier prediction system via Chou's general PseAAC, Predicting apoptosis protein subcellular localization by integrating auto-cross correlation and PSSM into Chou's PseAAC, pLoc\_bal-mGneg: predict subcellular localization of Gram-negative bacterial proteins by quasi-balancing training dataset and general PseAAC, Identify Gram-negative bacterial secreted protein types by incorporating different modes of PSSM into Chou's general PseAAC via Kullback-Leibler divergence, Predicting structural classes of proteins by incorporating their global and local physicochemical and conformational properties into general Chou's PseAAC, Large-scale frequent stem pattern mining in RNA families, iMethyl-STTNC: identification of N\(^6\)-methyladenosine sites by extending the idea of SAAC into Chou's PseAAC to formulate RNA sequences, Predicting membrane protein types by incorporating a novel feature set into Chou's general PseAAC, Analysis and prediction of ion channel inhibitors by using feature selection and Chou's general pseudo amino acid composition, CE-PLoc: An ensemble classifier for predicting protein subcellular locations by fusing different modes of pseudo amino acid composition, Predicting membrane protein types by incorporating protein topology, domains, signal peptides, and physicochemical properties into the general form of Chou's pseudo amino acid composition, Characterization of structure-antioxidant activity relationship of peptides in free radical systems using QSAR models: key sequence positions and their amino acid properties, A novel statistical measure for sequence comparison on the basis of \(k\)-word counts, Protein space: a natural method for realizing the nature of protein universe, Predicting promoters by pseudo-trinucleotide compositions based on discrete wavelets transform, A feature extraction technique using bi-gram probabilities of position specific scoring matrix for protein fold recognition, QSAR prediction of HIV-1 protease inhibitory activities using docking derived molecular descriptors, Effective DNA binding protein prediction by using key features via Chou's general PseAAC, iPPI-PseAAC(CGR): identify protein-protein interactions by incorporating chaos game representation into PseAAC, Fu-SulfPred: identification of protein S-sulfenylation sites by fusing forests via Chou's general PseAAC, Prediction and functional analysis of prokaryote lysine acetylation site by incorporating six types of features into Chou's general PseAAC, pSSbond-PseAAC: prediction of disulfide bonding sites by integration of PseAAC and statistical moments, MFSC: multi-voting based feature selection for classification of Golgi proteins by adopting the general form of Chou's PseAAC components, Analysis and prediction of animal toxins by various Chou's pseudo components and reduced amino acid compositions, 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, iRNA-PseKNC(2methyl): identify RNA 2'-O-methylation sites by convolution neural network and Chou's pseudo components, Identifying N\(^6\)-methyladenosine sites using extreme gradient boosting system optimized by particle swarm optimizer, SPrenylC-PseAAC: a sequence-based model developed via Chou's 5-steps rule and general PseAAC for identifying S-prenylation sites in proteins, Dforml(KNN)-PseAAC: detecting formylation sites from protein sequences using K-nearest neighbor algorithm via Chou's 5-step rule and pseudo components, Prediction of interface residue based on the features of residue interaction network, Highly accurate prediction of protein self-interactions by incorporating the average block and PSSM information into the general PseAAC, Bi-PSSM: position specific scoring matrix based intelligent computational model for identification of mycobacterial membrane 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, MemHyb: predicting membrane protein types by hybridizing SAAC and PSSM, 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, Optimal atomic-resolution structures of prion AGAAAAGA amyloid fibrils, Self-similarity analysis of eubacteria genome based on weighted graph, Knowledge-based virtual screening of HLA-A*0201-restricted CD8\(^+\) T-cell epitope peptides from herpes simplex virus genome, Two-intermediate model to characterize the structure of fast-folding proteins, Predicting mycobacterial proteins subcellular locations by incorporating pseudo-average chemical shift into the general form of Chou's pseudo amino acid composition, A segmented principal component analysis -- regression approach to QSAR study of peptides, RFCRYS: sequence-based protein crystallization propensity prediction by means of random forest, \textbf{iLoc-Virus}: a multi-label learning classifier for identifying the subcellular localization of virus proteins with both single and multiple sites, A novel canonical dual computational approach for prion AGAAAAGA amyloid fibril molecular modeling, Studies on the rules of \(\beta\)-strand alignment in a protein \(\beta\)-sheet structure, BacPP: bacterial promoter prediction -- a tool for accurate sigma-factor specific assignment in enterobacteria, Disease embryo development network reveals the relationship between disease genes and embryo development genes, \textit{In vitro} transcriptomic prediction of hepatotoxicity for early drug discovery, Predicting protein subchloroplast locations with both single and multiple sites via three different modes of Chou's pseudo amino acid compositions, Discriminating bioluminescent proteins by incorporating average chemical shift and evolutionary information into the general form of Chou's pseudo amino acid composition, Analysis of codon use features of stearoyl-acyl carrier protein desaturase gene in \textit{Camellia sinensis}, Interrogating noise in protein sequences from the perspective of protein-protein interactions prediction, Phogly-PseAAC: prediction of lysine phosphoglycerylation in proteins incorporating with position-specific propensity, Discriminate protein decoys from native by using a scoring function based on ubiquitous phi and psi angles computed for all atom, Prediction of Golgi-resident protein types using general form of Chou's pseudo-amino acid compositions: approaches with minimal redundancy maximal relevance feature selection, Machine learning approaches for discrimination of extracellular matrix proteins using hybrid feature space, Identify five kinds of simple super-secondary structures with quadratic discriminant algorithm based on the chemical shifts, Using weighted features to predict recombination hotspots in \textit{Saccharomyces cerevisiae}, 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, Prediction of protein structure classes by incorporating different protein descriptors into general Chou's pseudo amino acid composition, Classification of membrane protein types using voting feature interval in combination with Chou's pseudo amino acid composition, iLM-2L: a two-level predictor for identifying protein lysine methylation sites and their methylation degrees by incorporating K-gap amino acid pairs into Chou's general PseAAC, Identification of hormone binding proteins based on machine learning methods, Predicting S-nitrosylation proteins and sites by fusing multiple features, GOASVM: a subcellular location predictor by incorporating term-frequency gene ontology into the general form of Chou's pseudo-amino acid composition, A two-layer classification framework for protein fold recognition, Prediction of \(\beta\)-lactamase and its class by Chou's pseudo-amino acid composition and support vector machine, Discrimination of acidic and alkaline enzyme using Chou's pseudo amino acid composition in conjunction with probabilistic neural network model, Novel 3D bio-macromolecular bilinear descriptors for protein science: predicting protein structural classes, VR-BFDT: a variance reduction based binary fuzzy decision tree induction method for protein function prediction, Predicting Gram-positive bacterial protein subcellular localization based on localization motifs, Efficacy of function specific 3D-motifs in enzyme classification according to their EC-numbers, 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, Predicting anticancer peptides with Chou's pseudo amino acid composition and investigating their mutagenicity via ames test, Improving the prediction accuracy of protein structural class: approached with alternating word frequency and normalized Lempel-Ziv complexity, A QSPR-like model for multilocus genotype networks of \textit{Fasciola hepatica} in Northwest Spain, Predicting DNA binding proteins using support vector machine with hybrid fractal features, Accurate prediction of protein structural classes by incorporating predicted secondary structure information into the general form of Chou's pseudo amino acid composition, A two-stage SVM method to predict membrane protein types by incorporating amino acid classifications and physicochemical properties into a general form of Chou's PseAAC, Prediction of posttranslational modification sites from amino acid sequences with kernel methods, Robust feature generation for protein subchloroplast location prediction with a weighted GO transfer model, A protein structural classes prediction method based on PSI-BLAST profile, Using protein granularity to extract the protein sequence features, A Hooke's law-based approach to protein folding rate, Protein fold recognition by alignment of amino acid residues using kernelized dynamic time warping, Chou's pseudo amino acid composition improves sequence-based antifreeze protein prediction, Constructing a linear QSAR for some metabolizable drugs by human or pig flavin-containing monooxygenases using some molecular features selected by a genetic algorithm trained SVM, Neural network and SVM classifiers accurately predict lipid binding proteins, irrespective of sequence homology, Prediction of the determinants of thermal stability by linear discriminant analysis: the case of the glutamate dehydrogenase protein family, Human proteins characterization with subcellular localizations, An effective haplotype assembly algorithm based on hypergraph partitioning, Transmission of intra-cellular genetic information: a system proposal, A set of descriptors for identifying the protein-drug interaction in cellular networking, A new technique for generating pathogenic barcodes in breast cancer susceptibility analysis, Prediction of antioxidant proteins by incorporating statistical moments based features into Chou's PseAAC, Predicting protein sub-Golgi locations by combining functional domain enrichment scores with pseudo-amino acid compositions, Rational design, conformational analysis and membrane-penetrating dynamics study of Bac2A-derived antimicrobial peptides against gram-positive clinical strains isolated from pyemia, A Novel Fast Approach for Protein Classification and Evolutionary Analysis, DNA-binding protein prediction based on deep transfer learning

Uses Software

Cites Work

Retrieved from "https://portal.mardi4nfdi.de/w/index.php?title=Publication:1670702&oldid=13982035"