Using LogitBoost classifier to predict protein structural classes

DOI10.1016/j.jtbi.2005.05.034zbMath1445.92220OpenAlexW2008343108WikidataQ51968344 ScholiaQ51968344MaRDI QIDQ2194896

Kuo-Chen Chou, Kai-Yan Feng, Wen-Cong Lu, Yu-Dong Cai

Publication date: 7 September 2020

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

Full work available at URL: https://doi.org/10.1016/j.jtbi.2005.05.034

zbMATH Keywords

support vector machinesprotein structure classificationamino acid compositionLogitBoost

Mathematics Subject Classification ID

Protein sequences, DNA sequences (92D20) Software, source code, etc. for problems pertaining to biology (92-04)

Related Items

A novel feature representation method based on Chou's pseudo amino acid composition for protein structural class prediction ⋮ Novel 3D bio-macromolecular bilinear descriptors for protein science: predicting protein structural classes ⋮ Improving the prediction accuracy of protein structural class: approached with alternating word frequency and normalized Lempel-Ziv complexity ⋮ Prediction of protein structure classes using hybrid space of multi-profile Bayes and bi-gram probability feature spaces ⋮ Using protein granularity to extract the protein sequence features ⋮ Using stacked generalization to predict membrane protein types based on pseudo-amino acid composition ⋮ Using pseudo-amino acid composition and support vector machine to predict protein structural class ⋮ BlaPred: predicting and classifying \(\beta\)-lactamase using a 3-tier prediction system via Chou's general PseAAC ⋮ pLoc\_bal-mGneg: predict subcellular localization of Gram-negative bacterial proteins by quasi-balancing training dataset and general PseAAC ⋮ Predicting structural classes of proteins by incorporating their global and local physicochemical and conformational properties into general Chou's PseAAC ⋮ iPPI-PseAAC(CGR): identify protein-protein interactions by incorporating chaos game representation into PseAAC ⋮ iRNA-PseKNC(2methyl): identify RNA 2'-O-methylation sites by convolution neural network and Chou's pseudo components ⋮ Predicting protein structural class based on multi-features fusion ⋮ LEGO-based generalized set of two linear algebraic 3D bio-macro-molecular descriptors: theory and validation by QSARs

Uses Software

• AdaBoost.MH
• LogitBoost

Cites Work

• Unnamed Item
• SLLE for predicting membrane protein types
• Using decision trees to construct a practical parser
• A decision-theoretic generalization of on-line learning and an application to boosting
• Arcing classifiers. (With discussion)
• Additive logistic regression: a statistical view of boosting. (With discussion and a rejoinder by the authors)
• Improved boosting algorithms using confidence-rated predictions
• Identify catalytic triads of serine hydrolases by support vector machines
• Soft margins for AdaBoost