ArticleInternational journal of molecular sciences2022
Comprehensive Collection and Prediction of ABC Transmembrane Protein Structures in the AI Era of Structural Biology.
Article in International journal of molecular sciences, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 26 citations in OpenAlex.
- 3DSeqCheck: A Web-based Tool for Verifying Sequence Consistency Between a 3D Structure File and the Corresponding UniProt Entry.Journal of molecular biology · 2026Article
- Characterization of the YCjN ABC Transporter in Escherichia coli: Role in Maltose and Ethidium Bromide Transport.Molecular biotechnology · 2026Article
- Infant gut anellovirus composition associates with early life factors and childhood atopic disease.Nature communications · 2025Article
- SeaMoon: From protein language models to continuous structural heterogeneity.Structure (London, England : 1993) · 2025Article
- Message hidden in α-helices-toward a better understanding of plant ABCG transporters' multispecificity.Plant physiology · 2025Article
- Challenges in bridging the gap between protein structure prediction and functional interpretation.Proteins · 2025Article
- SARS-CoV-2 envelope protein alters calcium signaling via SERCA interactions.Scientific reports · 2024Article
- Explaining Conformational Diversity in Protein Families through Molecular Motions.Scientific data · 2024Article
- A dimeric holin/antiholin complex controls lysis by phage T4.Frontiers in microbiology · 2024Article
- Genome wide structural prediction of ABC transporter systems inFrontiers in microbiology · 2024Article
- Folding correctors can restore CFTR posttranslational folding landscape by allosteric domain-domain coupling.Nature communications · 2023Article
- Genetics ofCancers · 2023Review
- 3D-Beacons: decreasing the gap between protein sequences and structures through a federated network of protein structure data resources.GigaScience · 2022Article
- The Reentry Helix Is Potentially Involved in Cholesterol Sensing of the ABCG1 Transporter Protein.International journal of molecular sciences · 2022Article
- AI-Based Protein Interaction Screening and Identification (AISID).International journal of molecular sciences · 2022Article
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 2 countries.
Funding
Abstract
The number of unique transmembrane (TM) protein structures doubled in the last four years, which can be attributed to the revolution of cryo-electron microscopy. In addition, AlphaFold2 (AF2) also provided a large number of predicted structures with high quality. However, if a specific protein family is the subject of a study, collecting the structures of the family members is highly challenging in spite of existing general and protein domain-specific databases. Here, we demonstrate this and assess the applicability and usability of automatic collection and presentation of protein structures via the ABC protein superfamily. Our pipeline identifies and classifies transmembrane ABC protein structures using the PFAM search and also aims to determine their conformational states based on special geometric measures, conftors. Since the AlphaFold database contains structure predictions only for single polypeptide chains, we performed AF2-Multimer predictions for human ABC half transporters functioning as dimers. Our AF2 predictions warn of possibly ambiguous interpretation of some biochemical data regarding interaction partners and call for further experiments and experimental structure determination. We made our predicted ABC protein structures available through a web application, and we joined the 3D-Beacons Network to reach the broader scientific community through platforms such as PDBe-KB.
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Registered trials
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