ArticleNucleic acids research2013
PDBTM: Protein Data Bank of transmembrane proteins after 8 years.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 147 papers.
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147 citing papers in PubMed, 299 citations in OpenAlex.
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- Engineered Channel Asymmetry Extends Hydrogen-Bonding Networks for Proton Conduction.bioRxiv : the preprint server for biology · 2026Article
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- Ensemble-conditioned protein sequence design with Caliby.bioRxiv : the preprint server for biology · 2025Article
- Capturing the native structure of membrane proteins using vesicles.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- TmDet 4.0: determining membrane orientation of transmembrane proteins from 3D structure.Nucleic acids research · 2025Article
- Transmembrane Homodimers Interface Identification: Predicting Interface Residues in Alpha-Helical Transmembrane Protein Homodimers Using Sequential and Structural Features.International journal of molecular sciences · 2025Article
- Mapping O- and N-Glycosylation in Transmembrane and Interface Regions of Proteins: Insights from a Database Search Study.International journal of molecular sciences · 2025Article
- Illustrative Features and Utilities of MPAD: Thermodynamic Database for Membrane Protein-Protein Complexes.Methods in molecular biology (Clifton, N.J.) · 2025Article
- A Survey of Current Status in AI-Based Topology Prediction of Transmembrane Proteins.Methods in molecular biology (Clifton, N.J.) · 2025Article
- PLMC: Language Model of Protein Sequences Enhances Protein Crystallization Prediction.Interdisciplinary sciences, computational life sciences · 2024Article
- AIUPred: combining energy estimation with deep learning for the enhanced prediction of protein disorder.Nucleic acids research · 2024Article
- Improving AlphaFold Predicted Contacts for Alpha-Helical Transmembrane Proteins Using Structural Features.International journal of molecular sciences · 2024Article
- EncoMPASS: An encyclopedia of membrane proteins analyzed by structure and symmetry.Structure (London, England : 1993) · 2024Article
- Modeling membrane geometries implicitly in Rosetta.Protein science : a publication of the Protein Society · 2024Article
- Elucidating molecular mechanisms of protoxin-II state-specific binding to the human NaV1.7 channel.The Journal of general physiology · 2024Article
87 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The PDBTM database (available at http://pdbtm.enzim.hu), the first comprehensive and up-to-date transmembrane protein selection of the Protein Data Bank, was launched in 2004. The database was created and has been continuously updated by the TMDET algorithm that is able to distinguish between transmembrane and non-transmembrane proteins using their 3D atomic coordinates only. The TMDET algorithm can locate the spatial positions of transmembrane proteins in lipid bilayer as well. During the last 8 years not only the size of the PDBTM database has been steadily growing from ∼400 to 1700 entries but also new structural elements have been identified, in addition to the well-known α-helical bundle and β-barrel structures. Numerous 'exotic' transmembrane protein structures have been solved since the first release, which has made it necessary to define these new structural elements, such as membrane loops or interfacial helices in the database. This article reports the new features of the PDBTM database that have been added since its first release, and our current efforts to keep the database up-to-date and easy to use so that it may continue to serve as a fundamental resource for the scientific community.
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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.