ArticleNucleic acids research2015
Expediting topology data gathering for the TOPDB database.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- A Co-attention Mechanism of Jointly Capturing Sequence and Structure Features for Signal Peptide Prediction.Computational and structural biotechnology journal · 2026Article
- Prediction of pathogenic mutations in human transmembrane proteins and their associated diseases via utilizing pre-trained Bio-LLMs.Communications biology · 2025Article
- The 2024 Nucleic Acids Research database issue and the online molecular biology database collection.Nucleic acids research · 2024Article
- UniTmp: unified resources for transmembrane proteins.Nucleic acids research · 2024Article
- TSignal: a transformer model for signal peptide prediction.Bioinformatics (Oxford, England) · 2023Article
- Comprehensive Discovery of the Accessible Primary Amino Group-Containing Segments from Cell Surface Proteins by Fine-Tuning a High-Throughput Biotinylation Method.International journal of molecular sciences · 2022Article
- The Cancer Surfaceome Atlas integrates genomic, functional and drug response data to identify actionable targets.Nature cancer · 2021Article
- TMSNP: a web server to predict pathogenesis of missense mutations in the transmembrane region of membrane proteins.NAR genomics and bioinformatics · 2021Article
- OMPdb: A Global Hub of Beta-Barrel Outer Membrane Proteins.Frontiers in bioinformatics · 2021Article
- Quantitative Analysis of Multiplex H-Bonds.Journal of the American Chemical Society · 2020Article
- Partial proteolysis improves the identification of the extracellular segments of transmembrane proteins by surface biotinylation.Scientific reports · 2020Article
- Covalently modified carboxyl side chains on cell surface leads to a novel method toward topology analysis of transmembrane proteins.Scientific reports · 2019Article
- SignalP 5.0 improves signal peptide predictions using deep neural networks.Nature biotechnology · 2019Article
- Charged residues next to transmembrane regions revisited: "Positive-inside rule" is complemented by the "negative inside depletion/outside enrichment rule".BMC biology · 2017Article
- Identification of Extracellular Segments by Mass Spectrometry Improves Topology Prediction of Transmembrane Proteins.Scientific reports · 2017Article
- Identification of LukPQ, a novel, equid-adapted leukocidin of Staphylococcus aureus.Scientific reports · 2017Article
- TSTMP: target selection for structural genomics of human transmembrane proteins.Nucleic acids research · 2017Article
- Membranome: a database for proteome-wide analysis of single-pass membrane proteins.Nucleic acids research · 2017Article
- TOPDOM: database of conservatively located domains and motifs in proteins.Bioinformatics (Oxford, England) · 2016Article
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4 authors.
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Abstract
The Topology Data Bank of Transmembrane Proteins (TOPDB, http://topdb.enzim.ttk.mta.hu) contains experimentally determined topology data of transmembrane proteins. Recently, we have updated TOPDB from several sources and utilized a newly developed topology prediction algorithm to determine the most reliable topology using the results of experiments as constraints. In addition to collecting the experimentally determined topology data published in the last couple of years, we gathered topographies defined by the TMDET algorithm using 3D structures from the PDBTM. Results of global topology analysis of various organisms as well as topology data generated by high throughput techniques, like the sequential positions of N- or O-glycosylations were incorporated into the TOPDB database. Moreover, a new algorithm was developed to integrate scattered topology data from various publicly available databases and a new method was introduced to measure the reliability of predicted topologies. We show that reliability values highly correlate with the per protein topology accuracy of the utilized prediction method. Altogether, more than 52,000 new topology data and more than 2600 new transmembrane proteins have been collected since the last public release of the TOPDB database.
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