A method for discovering transmembrane beta-barrel proteins in Gram-negative bacterial proteomes

DOI10.1016/J.COMPBIOLCHEM.2008.03.010MaRDI QIDQ1004939zbMATH OpenOpenAlexWikidataFDO

Authors Jing Hu, Changhui Yan

Publication date 12 March 2009

Published in Computational Biology and Chemistry (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1016/j.compbiolchem.2008.03.010

zbMATH Keywords

\(k\)-nearest neighborbeta-barrelpredictionweighted Euclidian distance

Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10) Biochemistry, molecular biology (92C40)

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Cited in

(12)

• Statistical analysis and exposure status classification of transmembrane beta barrel residues
• TMBETADISC-RBF: discrimination of \(\beta\)-barrel membrane proteins using RBF networks and PSSM profiles
• Identify Gram-negative bacterial secreted protein types by incorporating different modes of PSSM into Chou's general PseAAC via Kullback-Leibler divergence
• Predicting the ligand-binding properties of \textit{Borrelia burgdorferi} s.s. Bmp proteins in light of the conserved features of related \textit{Borrelia} proteins
• In silico analysis of antibody triggering biofilm associated protein in \textit{Acinetobacter baumannii}
• Ligand-binding prediction in the resistance-nodulation-cell division (RND) proteins
• On permuted super-secondary structures of transmembrane \(\beta\)-barrel proteins
• A proteome-wide analysis of domain architectures of prokaryotic single-spanning transmembrane proteins
• Scoring hidden Markov models to discriminate \(\beta\)-barrel membrane proteins
• ConPred\_elite: a highly reliable approach to transmembrane topology prediction
• Identification of novel type III effectors using latent Dirichlet allocation
• \(\beta\)-barrel transmembrane proteins: geometric modelling, detection of transmembrane region, and structural properties

Describes a project that uses

Uses Software

• PSI-BLAST
• PROFtmb
• Psortb
• BOMP
• PRED-TMBB
• TMB-Hunt
• BLAST

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