ArticleProceedings of the National Academy of Sciences of the United States of America2018
High-resolution structure prediction of
Article in Proceedings of the National Academy of Sciences of the United States of America, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Thermal transport across membranes and the Kapitza length from photothermal microscopy.Journal of biological physics · 2023Article
- General features of transmembrane beta barrels from a large database.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Article
- Computational prediction of extracellular loops of the Por39 outer membrane porin ofComputational and structural biotechnology journal · 2023Article
- 3D-BMPP: 3D Beta-Barrel Membrane Protein Predictor.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Thermodynamics of unfolding mechanisms of mouse mammary tumor virus pseudoknot from a coarse-grained loop-entropy model.Journal of biological physics · 2022Article
- Dawn of a New Era for Membrane Protein Design.Biodesign research · 2022Review
- Computational structure prediction provides a plausible mechanism for electron transfer by the outer membrane protein Cyc2 from Acidithiobacillus ferrooxidans.Protein science : a publication of the Protein Society · 2021Article
- Model of Environmental Membrane Field for Transmembrane Proteins.International journal of molecular sciences · 2021Article
- Label-free imaging of fibroblast membrane interfaces and protein signatures with vibrational infrared photothermal and phase signals.Biomedical optics express · 2021Article
- GeTFEP: A general transfer free energy profile of transmembrane proteins.Protein science : a publication of the Protein Society · 2020Article
- EpitoCore: Mining Conserved Epitope Vaccine Candidates in the Core Proteome of Multiple Bacteria Strains.Frontiers in immunology · 2020Article
- Understanding Conformational Dynamics of Complex Lipid Mixtures Relevant to Biology.The Journal of membrane biology · 2018Review
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Authors and funding
5 authors.
Funding
Abstract
[Formula: see text]-Barrel membrane proteins ([Formula: see text]MPs) play important roles, but knowledge of their structures is limited. We have developed a method to predict their 3D structures. We predict strand registers and construct transmembrane (TM) domains of [Formula: see text]MPs accurately, including proteins for which no prediction has been attempted before. Our method also accurately predicts structures from protein families with a limited number of sequences and proteins with novel folds. An average main-chain rmsd of 3.48 Å is achieved between predicted and experimentally resolved structures of TM domains, which is a significant improvement ([Formula: see text]3 Å) over a recent study. For [Formula: see text]MPs with NMR structures, the deviation between predictions and experimentally solved structures is similar to the difference among the NMR structures, indicating excellent prediction accuracy. Moreover, we can now accurately model the extended [Formula: see text]-barrels and loops in non-TM domains, increasing the overall coverage of structure prediction by [Formula: see text]%. Our method is general and can be applied to genome-wide structural prediction of [Formula: see text]MPs.
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Registered trials
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