ArticleJournal of chemical information and modeling2017
Determination of Hydrophobic Lengths of Membrane Proteins with the HDGB Implicit Membrane Model.
Article in Journal of chemical information and modeling, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.The journal of physical chemistry. B · 2024Review
- Common synaptic phenotypes arising from diverse mutations in the human NMDA receptor subunit GluN2A.Communications biology · 2022Article
- Spatial arrangement of proteins in planar and curved membranes by PPM 3.0.Protein science : a publication of the Protein Society · 2022Article
- Diverse Scientific Benchmarks for Implicit Membrane Energy Functions.Journal of chemical theory and computation · 2021Article
- Protein Structure Prediction and Design in a Biologically Realistic Implicit Membrane.Biophysical journal · 2020Article
- Generalized Born Implicit Solvent Models for Biomolecules.Annual review of biophysics · 2019Review
- Article
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2 authors.
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Abstract
A protocol for predicting the hydrophobic length of membrane proteins using the heterogeneous dielectric generalized Born (HDGB) implicit membrane model is presented. The method involves optimal positioning in the membrane and identification of lipid-facing and inward-facing residues, followed by energy optimization of the implicit membrane model to obtain the hydrophobic length from the optimal membrane width. The latest HDGB version 3 (HDGBv3) and HDGB van der Waals (HDGBvdW) models were applied to a test set containing 15 proteins (seven β-barrel and eight α-helical proteins), for which matching membrane widths are available from experiment, and an additional set contains ten α-helical and ten β-barrel proteins without any experimental data. The results with the HDGB model compare favorably with predictions from methods used in the Orientations of Proteins in Membranes (OPM) and Protein Data Bank of Transmembrane Proteins (PDB-TM) databases.
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