ArticleJournal of computational chemistry2017
Heterogeneous dielectric generalized Born model with a van der Waals term provides improved association energetics of membrane-embedded transmembrane helices.
Article in Journal of computational chemistry, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.The journal of physical chemistry. B · 2024Review
- Heterogeneous Dielectric Implicit Membrane Model for the Calculation of MMPBSA Binding Free Energies.Journal of chemical information and modeling · 2019Article
- Generalized Born Implicit Solvent Models for Biomolecules.Annual review of biophysics · 2019Review
- Article
- Determination of Hydrophobic Lengths of Membrane Proteins with the HDGB Implicit Membrane Model.Journal of chemical information and modeling · 2017Article
- Discrimination of Native-like States of Membrane Proteins with Implicit Membrane-based Scoring Functions.Journal of chemical theory and computation · 2017Article
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3 authors.
Funding
Abstract
The heterogeneous dielectric generalized Born (HDGB) implicit membrane formalism is extended by the addition of a van der Waals dispersion term to better describe the nonpolar components of the free energy of solvation. The new model, termed HDGBvdW, improves the energy estimates in the hydrophobic interior of the membrane, where polar and charged species are rarely found and nonpolar interactions become significant. The implicit van der Waals term for the membrane environment extends the model from Gallicchio et al. (J. Comput. Chem. 2004, 25, 479) by combining separate contributions from each of the membrane components. The HDGBvdW model is validated with a series of test cases ranging from membrane insertion and pair association profiles of amino acid side chain analogs and transmembrane helices. Overall, the HDGBvdW model leads to increased agreement with explicit membrane simulation results and experimental data. © 2016 Wiley Periodicals, Inc.
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