Determination of Hydrophobic Lengths of Membrane Proteins with the HDGB Implicit Membrane Model.
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ABSTRACT:
SUBMITTER: Dutagaci B
PROVIDER: S-EPMC5743600 | biostudies-literature | 2017 Dec
REPOSITORIES: biostudies-literature
Publications
Determination of Hydrophobic Lengths of Membrane Proteins with the HDGB Implicit Membrane Model.
Dutagaci Bercem B Feig Michael M
Journal of chemical information and modeling 20171201 12
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 appli ...[more]
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