ArticleNucleic acids research2004
Predicting transmembrane beta-barrels in proteomes.
Article in Nucleic acids research, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
57 citing papers in PubMed.
- The Name Is Barrel, β-Barrel.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Protein Sorting Prediction.Methods in molecular biology (Clifton, N.J.) · 2024Article
- The Functionality of Membrane-Inserting Proteins and Peptides: Curvature Sensing, Generation, and Pore Formation.The Journal of membrane biology · 2023Review
- TMbed: transmembrane proteins predicted through language model embeddings.BMC bioinformatics · 2022Article
- Three-Dimensional Structure Characterization and Inhibition Study of Exfoliative Toxin D FromFrontiers in pharmacology · 2022Article
- Computational prediction of secreted proteins in gram-negative bacteria.Computational and structural biotechnology journal · 2021Review
- Modeling aspects of the language of life through transfer-learning protein sequences.BMC bioinformatics · 2019Article
- A Brief History of Protein Sorting Prediction.The protein journal · 2019Review
- Genome Report: Identification and Validation of Antigenic Proteins fromG3 (Bethesda, Md.) · 2017Article
- Identification of New Features from Known Bacterial Protective Vaccine Antigens Enhances Rational Vaccine Design.Frontiers in immunology · 2017Article
- Computational Approaches for Revealing the Structure of Membrane Transporters: Case Study on Bilitranslocase.Computational and structural biotechnology journal · 2017Review
- Mapping the membrane proteome of anaerobic gut fungi identifies a wealth of carbohydrate binding proteins and transporters.Microbial cell factories · 2016Article
- TMSEG: Novel prediction of transmembrane helices.Proteins · 2016Article
- Translatomics combined with transcriptomics and proteomics reveals novel functional, recently evolved orphan genes in Escherichia coli O157:H7 (EHEC).BMC genomics · 2016Article
- Mosaic composition of ribA and wspB genes flanking the virB8-D4 operon in the Wolbachia supergroup B-strain, wStr.Archives of microbiology · 2016Article
- Evidence for the recent origin of a bacterial protein-coding, overlapping orphan gene by evolutionary overprinting.BMC evolutionary biology · 2015Article
- The C-terminus of Bienertia sinuspersici Toc159 contains essential elements for its targeting and anchorage to the chloroplast outer membrane.Frontiers in plant science · 2014Article
- Article
- Ferric-pyoverdine recognition by Fpv outer membrane proteins of Pseudomonas protegens Pf-5.Journal of bacteriology · 2013Article
- TMBB-DB: a transmembrane β-barrel proteome database.Bioinformatics (Oxford, England) · 2012Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
Very few methods address the problem of predicting beta-barrel membrane proteins directly from sequence. One reason is that only very few high-resolution structures for transmembrane beta-barrel (TMB) proteins have been determined thus far. Here we introduced the design, statistics and results of a novel profile-based hidden Markov model for the prediction and discrimination of TMBs. The method carefully attempts to avoid over-fitting the sparse experimental data. While our model training and scoring procedures were very similar to a recently published work, the architecture and structure-based labelling were significantly different. In particular, we introduced a new definition of beta- hairpin motifs, explicit state modelling of transmembrane strands, and a log-odds whole-protein discrimination score. The resulting method reached an overall four-state (up-, down-strand, periplasmic-, outer-loop) accuracy as high as 86%. Furthermore, accurately discriminated TMB from non-TMB proteins (45% coverage at 100% accuracy). This high precision enabled the application to 72 entirely sequenced Gram-negative bacteria. We found over 164 previously uncharacterized TMB proteins at high confidence. Database searches did not implicate any of these proteins with membranes. We challenge that the vast majority of our 164 predictions will eventually be verified experimentally. All proteome predictions and the PROFtmb prediction method are available at http://www.rostlab.org/ services/PROFtmb/.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.