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PreprintCited by 4Protein Structure and DynamicsMachine Learning in BioinformaticsEnzyme Structure and Function

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TMVisDB: Annotation and 3D-visualization of transmembrane proteins

Open access
Olenyi, Tobias, Marquet, Céline, Grekova, Anastasia, Houri, Leen, Heinzinger, Michael, Dallago, Christian, Rost, Burkhard·2024·Journal of Molecular Biology
DOI 10.1101/2024.11.22.624323

Preprint — published as 10.1016/j.jmb.2025.168997 · Paper page

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Abstract

Since the rise of cellular life, transmembrane proteins (TMPs) have been crucial to various cellular processes through their central role as gates and gatekeepers. Despite their importance, experimental high-resolution structures for TMPs remain underrepresented due to experimental challenges. Given its performance leap, structure predictions have begun to close the gap. However, identifying the membrane regions and topology in three-dimensional structure files on a large scale still requires additional in silico predictions. Here, we introduce TMVisDB to sieve through millions of predicted structures for TMPs. This resource enables both browsing through 46 million predicted TMPs and visualizing them along with their topological annotations without having to tap into costly predictions of the AlphaFold3-style. TMVisDB joins AlphaFoldDB structure predictions and transmembrane topology predictions from the protein language model (pLM) based method TMbed . We showcase the utility of TMVisDB for the analysis of proteins through two use cases, namely the B-lymphocyte antigen CD 20 ( Homo sapiens ) and the cellulose synthase ( Novosphingobium sp. P6W ). We demonstrate the value of TMVisDB for large-scale analyses through findings pertaining to all TMPs predicted for the human proteome. TMVisDB is freely available at https://tmvisdb.rostlab.org

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Metadata

Authors
Olenyi, T., Marquet, C., Grekova, A., Houri, L., Heinzinger, M., Dallago, C., & Rost, B.
Affiliations
  • Technical University of Munich (DE)
  • European Molecular Biology Laboratory (DE)
Corresponding author
Olenyi, Tobias
ORCID
Venue
Journal of Molecular Biology
Publisher
openRxiv
Published
2024-11-23
Volume
437
Issue
15
Pages
168997-168997
ISSN
0022-2836 (ISSN-L)
DOI
10.1101/2024.11.22.624323
OpenAlex
W4407367450
Cited by
4
References
1
Citations by year
2026: 1 · 2025: 3
FWCI
1.21
Type
journal article
Language
en
Open access
Licence
Locations
  • Journal of Molecular Biology (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
  • PubMed (publishedVersion)
Funders
Bayerisches Staatsministerium für Bildung und Kultus, Wissenschaft und Kunst
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Machine Learning in Bioinformatics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
Keywords
transmembrane proteins, membrane protein structure prediction, transmembrane topology prediction, AlphaFold2, 3D visualization, protein databases, CD20, cellulose synthase, human proteome, protein language models
MeSH terms
Glucosyltransferases, Humans, Membrane Proteins, Models, Molecular, Protein Conformation, Software, Computational Biology, Databases, Protein, Molecular Sequence Annotation

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