Using Chou's amphiphilic pseudo-amino acid composition and support vector machine for prediction of enzyme subfamily classes
From MaRDI portal
Publication:2211634
DOI10.1016/j.jtbi.2007.06.001zbMath1451.92245OpenAlexW1980256262WikidataQ34650136 ScholiaQ34650136MaRDI QIDQ2211634
Xiao-Yong Zou, Xi-Bin Zhou, Zhan-Chao Li, Chao Chen
Publication date: 11 November 2020
Published in: Journal of Theoretical Biology (Search for Journal in Brave)
Full work available at URL: https://doi.org/10.1016/j.jtbi.2007.06.001
Applications of statistics to biology and medical sciences; meta analysis (62P10) Protein sequences, DNA sequences (92D20)
Related Items
Physics and chemistry-driven artificial neural network for predicting bioactivity of peptides and proteins and their design, Predicting protein fold pattern with functional domain and sequential evolution information, Using support vector machines to distinguish enzymes: approached by incorporating wavelet transform, Use of fuzzy clustering technique and matrices to classify amino acids and its impact to Chou's pseudo amino acid composition, Multi-target QPDR classification model for human breast and colon cancer-related proteins using star graph topological indices, Prediction of protein structural classes by recurrence quantification analysis based on chaos game representation, Predicting DNA- and RNA-binding proteins from sequences with kernel methods, A novel representation for apoptosis protein subcellular localization prediction using support vector machine, 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, Multiclass cancer classification by support vector machines with class-wise optimized genes and probability estimates, 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, 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, A protein fold classifier formed by fusing different modes of pseudo amino acid composition via PSSM, Efficacy of function specific 3D-motifs in enzyme classification according to their EC-numbers, Linear regression model of short \(k\)-word: a similarity distance suitable for biological sequences with various lengths, Kernel methods for phenotyping complex plant architecture, 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, A set of descriptors for identifying the protein-drug interaction in cellular networking, pLoc\_bal-mGneg: predict subcellular localization of Gram-negative bacterial proteins by quasi-balancing training dataset and general PseAAC, 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, Prediction of the parallel/antiparallel orientation of beta-strands using amino acid pairing preferences and support vector machines, iPPI-PseAAC(CGR): identify protein-protein interactions by incorporating chaos game representation into PseAAC, Protein classification using texture descriptors extracted from the protein backbone image, High performance set of PseAAC and sequence based descriptors for protein classification, SecretP: identifying bacterial secreted proteins by fusing new features into Chou's pseudo-amino acid composition, 2D-MH: a web-server for generating graphic representation of protein sequences based on the physicochemical properties of their constituent amino acids, A study of entropy/clarity of genetic sequences using metric spaces and fuzzy sets, Predicting ion channels and their types by the dipeptide mode of pseudo amino acid composition, MemHyb: predicting membrane protein types by hybridizing SAAC and PSSM, 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, Prediction of GABA\(_{\mathrm A}\) receptor proteins using the concept of Chou's pseudo-amino acid composition and support vector machine, 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, \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, \textit{In vitro} transcriptomic prediction of hepatotoxicity for early drug discovery, Prediction protein structural classes with pseudo-amino acid composition: approximate entropy and hydrophobicity pattern, Predicting protein subchloroplast locations with both single and multiple sites via three different modes of Chou's pseudo amino acid compositions, The modified Mahalanobis discriminant for predicting outer membrane proteins by using Chou's pseudo amino acid composition, Predicting protein structural class based on multi-features fusion, Predicting protein structural classes with pseudo amino acid composition: an approach using geometric moments of cellular automaton image, Natural/random protein classification models based on star network topological indices, LEGO-based generalized set of two linear algebraic 3D bio-macro-molecular descriptors: theory and validation by QSARs
Uses Software
Cites Work
- Prediction of protein subcellular location using hydrophobic patterns of amino acid sequence
- Support-vector networks
- Predicting enzyme family classes by hybridizing gene product composition and pseudo-amino acid composition
- Predicting membrane protein type by functional domain composition and pseudo-amino acid composition
- Using stacked generalization to predict membrane protein types based on pseudo-amino acid composition
- Fuzzy KNN for predicting membrane protein types from pseudo-amino acid composition
- Pseudo amino acid composition and multi-class support vector machines approach for conotoxin superfamily classification
- Using pseudo-amino acid composition and support vector machine to predict protein structural class
