ArticleBiophysical journal2020
Protein Structure Prediction and Design in a Biologically Realistic Implicit Membrane.
Article in Biophysical journal, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 46 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
46 citing papers in PubMed, 85 citations in OpenAlex.
- Computational protein stability analysis of SCN1A missense variants reveals domain-dependent stability patterns.Epilepsia open · 2026Article
- Membrane Protein Folding and Biogenesis: Insights from Single-Molecule Force Spectroscopy.Chemical reviews · 2026Review
- Implicit membrane for helical peptide selectivity toward bacterial membranes.Biophysical journal · 2026Article
- Mechanistic Insights into Human Defensin Antimicrobial Activity from Membrane Simulations.The Journal of membrane biology · 2026Article
- Recent advances in the pharmacology of voltage-gated ion channels.Pharmacological reviews · 2025Review
- Design principles of the common Gly-X6-Gly membrane protein building block.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Orthogonal replication with optogenetic selection evolves yeast JEN1 into a mevalonate transporter.Molecular systems biology · 2025Article
- Cholesterol allosteric modulation of the oxytocin receptor.Biophysical journal · 2025Article
- Harnessing Deep Learning Methods for Voltage-Gated Ion Channel Drug Discovery.Physiology (Bethesda, Md.) · 2025Review
- Advancing Membrane-Associated Protein Docking with Improved Sampling and Scoring in Rosetta.Journal of chemical theory and computation · 2024Article
- CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.The journal of physical chemistry. B · 2024Review
- Computational design of de novo bioenergetic membrane proteins.Biochemical Society transactions · 2024Review
- Delineating redox cooperativity in water-soluble and membrane multiheme cytochromes through protein design.Protein science : a publication of the Protein Society · 2024Article
- Advancing membrane-associated protein docking with improved sampling and scoring in Rosetta.bioRxiv : the preprint server for biology · 2024Article
- Validation of de novo designed water-soluble and transmembrane β-barrels by in silico folding and melting.Protein science : a publication of the Protein Society · 2024Article
- Three-Dimensional Interaction Homology: Deconstructing Residue-Residue and Residue-Lipid Interactions in Membrane Proteins.Molecules (Basel, Switzerland) · 2024Article
- De novo-designed transmembrane proteins bind and regulate a cytokine receptor.Nature chemical biology · 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
- Integrative analysis of pathogenic variants in glucose-6-phosphatase based on an AlphaFold2 model.PNAS nexus · 2024Article
Corrections and comments
- Erratum issued
Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Protein design is a powerful tool for elucidating mechanisms of function and engineering new therapeutics and nanotechnologies. Although soluble protein design has advanced, membrane protein design remains challenging because of difficulties in modeling the lipid bilayer. In this work, we developed an implicit approach that captures the anisotropic structure, shape of water-filled pores, and nanoscale dimensions of membranes with different lipid compositions. The model improves performance in computational benchmarks against experimental targets, including prediction of protein orientations in the bilayer, ΔΔG calculations, native structure discrimination, and native sequence recovery. When applied to de novo protein design, this approach designs sequences with an amino acid distribution near the native amino acid distribution in membrane proteins, overcoming a critical flaw in previous membrane models that were prone to generating leucine-rich designs. Furthermore, the proteins designed in the new membrane model exhibit native-like features including interfacial aromatic side chains, hydrophobic lengths compatible with bilayer thickness, and polar pores. Our method advances high-resolution membrane protein structure prediction and design toward tackling key biological questions and engineering challenges.
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Registered trials
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.