Prediction of the parallel/antiparallel orientation of beta-strands using amino acid pairing preferences and support vector machines

DOI10.1016/J.JTBI.2009.12.019zbMATH Open1406.92479OpenAlexW2064420001WikidataQ30383920 ScholiaQ30383920MaRDI QIDQ1715345FDOQ1715345

Ning Zhang, Tao Zhang, Ji-Shou Ruan, Guangyou Duan, Shan Gao

Publication date: 4 February 2019

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

Full work available at URL: https://doi.org/10.1016/j.jtbi.2009.12.019

zbMATH Keywords

machine learningprotein structureencoding matrix\(\beta\)-sheetstrand-to-strand interactions

Mathematics Subject Classification ID

Learning and adaptive systems in artificial intelligence (68T05) Protein sequences, DNA sequences (92D20)

Cites Work

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• The modified Mahalanobis discriminant for predicting outer membrane proteins by using Chou's pseudo amino acid composition
• Using Chou's amphiphilic pseudo-amino acid composition and support vector machine for prediction of enzyme subfamily classes
• Identify catalytic triads of serine hydrolases by support vector machines
• \(\gamma\)-Turn types prediction in proteins using the support vector machines

Cited In (4)

• Nucleotide's bilinear indices: novel bio-macromolecular descriptors for bioinformatics studies of nucleic acids. I: Prediction of paromomycin's affinity constant with HIV-1 \(\Psi\)-RNA packaging region
• Anti-parallel Coiled Coils Structure Prediction by Support Vector Machine Classification
• Studies on the rules of \(\beta\)-strand alignment in a protein \(\beta\)-sheet structure
• Prediction of \(\beta\)-turn types in protein by using composite vector

Uses Software

• LIBSVM
• Cell-PLoc
• PISCES
• FUGUE
• PFRES
• FoldRate
• GenThreader

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