Backbone Free Energy Estimator Applied to Viral Glycoproteins.

Backbone Free Energy Estimator Applied to Viral Glycoproteins.

Penner, Robert C;
Journal of computational biology : a journal of computational molecular cell biology 2020 Vol. 27 pp. 1495-1508
229
penner2020backbonejournal

Abstract

Earlier analysis of the Protein Data Bank derived the distribution of rotations from the plane of a protein hydrogen bond donor peptide group to the plane of its acceptor peptide group. The quasi Boltzmann formalism of Pohl-Finkelstein is employed to estimate free energies of protein elements with these hydrogen bonds, pinpointing residues with a high propensity for conformational change. This is applied to viral glycoproteins as well as capsids, where the 90th+ percentiles of free energies determine residues that correlate well with viral fusion peptides and other functional domains in known cases and thus provide a novel method for predicting these sites of importance as antiviral drug or vaccine targets in general. The method is implemented at https://bion-server.au.dk/hbonds/ from an uploaded Protein Data Bank file.

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0x95644003c57E6F55A65596E3D9Eac6813e3566dA
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253860
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10.1089/cmb.2020.0120
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