ArticleBMC bioinformatics2017
Computing structure-based lipid accessibility of membrane proteins with mp_lipid_acc in RosettaMP.
Article in BMC bioinformatics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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21 citing papers in PubMed, 33 citations in OpenAlex.
- Cholesterol allosteric modulation of the oxytocin receptor.Biophysical journal · 2025Article
- Three-Dimensional Interaction Homology: Deconstructing Residue-Residue and Residue-Lipid Interactions in Membrane Proteins.Molecules (Basel, Switzerland) · 2024Article
- Modeling membrane geometries implicitly in Rosetta.Protein science : a publication of the Protein Society · 2024Article
- Implicit model to capture electrostatic features of membrane environment.PLoS computational biology · 2024Article
- Interpreting the molecular mechanisms of disease variants in human transmembrane proteins.Biophysical journal · 2023Article
- Docking cholesterol to integral membrane proteins with Rosetta.PLoS computational biology · 2023Article
- Membrane contact probability: An essential and predictive character for the structural and functional studies of membrane proteins.PLoS computational biology · 2022Article
- Protein-Protein Docking: Past, Present, and Future.The protein journal · 2022Review
- Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks.Nature communications · 2021Article
- Diverse Scientific Benchmarks for Implicit Membrane Energy Functions.Journal of chemical theory and computation · 2021Article
- Protein Structure Prediction: Conventional and Deep Learning Perspectives.The protein journal · 2021Review
- Structural determinants of cholesterol recognition in helical integral membrane proteins.Biophysical journal · 2021Article
- Guardians of the Cell: State-of-the-Art of Membrane Proteins from a Computational Point-of-View.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Macromolecular modeling and design in Rosetta: recent methods and frameworks.Nature methods · 2020Review
- Protein Structure Prediction and Design in a Biologically Realistic Implicit Membrane.Biophysical journal · 2020Article
- MemBlob database and server for identifying transmembrane regions using cryo-EM maps.Bioinformatics (Oxford, England) · 2020Article
- A Membrane Burial Potential with H-Bonds and Applications to Curved Membranes and Fast Simulations.Biophysical journal · 2018Article
- Statistically derived asymmetric membrane potentials from α-helical and β-barrel membrane proteins.Scientific reports · 2018Article
- Web-accessible molecular modeling with Rosetta: The Rosetta Online Server that Includes Everyone (ROSIE).Protein science : a publication of the Protein Society · 2018Article
- Determination of Hydrophobic Lengths of Membrane Proteins with the HDGB Implicit Membrane Model.Journal of chemical information and modeling · 2017Article
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundMembrane proteins are underrepresented in structural databases, which has led to a lack of computational tools and the corresponding inappropriate use of tools designed for soluble proteins. For membrane proteins, lipid accessibility is an essential property. Although programs are available for sequence-based prediction of lipid accessibility and structure-based identification of solvent-accessible surface area, the latter does not distinguish between water accessible and lipid accessible residues in membrane proteins.
resultsHere we present mp_lipid_acc, the first method to identify lipid accessible residues from the protein structure, implemented in the RosettaMP framework and available as a webserver. Our method uses protein structures transformed in membrane coordinates, for instance from PDBTM or OPM databases, and a defined membrane thickness to classify lipid accessibility of residues. mp_lipid_acc is applicable to both α-helical and β-barrel membrane proteins of diverse architectures with or without water-filled pores and uses a concave hull algorithm for surface-residue classification. We further provide a manually curated benchmark dataset that can be used for further method development.
conclusionsWe present a novel tool to classify lipid accessibility from the protein structure, which is applicable to proteins of diverse architectures and achieves prediction accuracies of 90% on a manually curated database. mp_lipid_acc is part of the Rosetta software suite, available at www.rosettacommons.org . The webserver is available at http://rosie.graylab.jhu.edu/mp_lipid_acc/submit and the benchmark dataset is available at http://tinyurl.com/mp-lipid-acc-dataset .
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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.