ArticleProtein science : a publication of the Protein Society2001
Prediction of the transmembrane regions of beta-barrel membrane proteins with a neural network-based predictor.
Article in Protein science : a publication of the Protein Society, 2001. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- A Survey of Current Status in AI-Based Topology Prediction of Transmembrane Proteins.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Enhanced identification of membrane transport proteins: a hybrid approach combining ProtBERT-BFD and convolutional neural networks.Journal of integrative bioinformatics · 2023Article
- Computational prediction of secreted proteins in gram-negative bacteria.Computational and structural biotechnology journal · 2021Review
- Prediction of Transmembrane Regions, Cholesterol, and Ganglioside Binding Sites in Amyloid-Forming Proteins Indicate Potential for Amyloid Pore Formation.Frontiers in molecular neuroscience · 2021Article
- Integrative approach for detecting membrane proteins.BMC bioinformatics · 2020Article
- A Brief History of Protein Sorting Prediction.The protein journal · 2019Review
- Comparative Analysis of TM and Cytoplasmic β-barrel Conformations Using Joint Descriptor.Scientific reports · 2018Article
- Cryo-EM structure of the gasdermin A3 membrane pore.Nature · 2018Article
- Computational Approaches for Revealing the Structure of Membrane Transporters: Case Study on Bilitranslocase.Computational and structural biotechnology journal · 2017Review
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- Effects of climate change on Salmonella infections.Foodborne pathogens and disease · 2014Article
- TMBB-DB: a transmembrane β-barrel proteome database.Bioinformatics (Oxford, England) · 2012Article
- A graph-theoretic approach for classification and structure prediction of transmembrane β-barrel proteins.BMC genomics · 2012Article
- Legionella pneumophila LbtU acts as a novel, TonB-independent receptor for the legiobactin siderophore.Journal of bacteriology · 2011Article
- OMPdb: a database of {beta}-barrel outer membrane proteins from Gram-negative bacteria.Nucleic acids research · 2011Article
- Charting the proteome of Cryptosporidium parvum sporozoites using sequence similarity-based BLAST searching.Journal of veterinary science · 2009Article
- HHomp--prediction and classification of outer membrane proteins.Nucleic acids research · 2009Article
- Immunization of pigs to prevent disease in humans: construction and protective efficacy of a Salmonella enterica serovar Typhimurium live negative-marker vaccine.Infection and immunity · 2007Article
- Prediction of beta-barrel membrane proteins by searching for restricted domains.BMC bioinformatics · 2005Article
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5 authors.
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Abstract
A method based on neural networks is trained and tested on a nonredundant set of beta-barrel membrane proteins known at atomic resolution with a jackknife procedure. The method predicts the topography of transmembrane beta strands with residue accuracy as high as 78% when evolutionary information is used as input to the network. Of the transmembrane beta-strands included in the training set, 93% are correctly assigned. The predictor includes an algorithm of model optimization, based on dynamic programming, that correctly models eight out of the 11 proteins present in the training/testing set. In addition, protein topology is assigned on the basis of the location of the longest loops in the models. We propose this as a general method to fill the gap of the prediction of beta-barrel membrane proteins.
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