Protein space: a natural method for realizing the nature of protein universe

DOI10.1016/j.jtbi.2012.11.005zbMath1406.92224OpenAlexW2142446362WikidataQ45413146 ScholiaQ45413146MaRDI QIDQ1715121

Chenglong Yu, Shiu-Yuen Cheng, Mo Deng, Shek-Chung Yau, Rong L. He, Stephen Shing-Toung Yau

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.2012.11.005

zbMATH Keywords

phylogenynatural vectorprotein universe

Mathematics Subject Classification ID

Problems related to evolution (92D15) Applications of graph theory (05C90) Biochemistry, molecular biology (92C40) Protein sequences, DNA sequences (92D20)

Related Items (1)

Convex hull analysis of evolutionary and phylogenetic relationships between biological groups

Uses Software

• 2D-MH
• GPCR-2L
• iDNA-Prot
• SubChlo
• SecretP
• OligoPred
• iNR-PhysChem

Cites Work

• iDNA-Prot
• Comparison of biosequences
• 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
• 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
• 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
• 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
• 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
• The modified Mahalanobis discriminant for predicting outer membrane proteins by using Chou's pseudo amino acid composition
• A note on the metric properties of trees
• Using Chou's amphiphilic pseudo-amino acid composition and support vector machine for prediction of enzyme subfamily classes
• Application of density similarities to predict membrane protein types based on pseudo-amino acid composition

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