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PeptoGrid-Rescoring Function for AutoDock Vina to Identify New Bioactive Molecules from Short Peptide Libraries.

ABSTRACT: Peptides are promising drug candidates due to high specificity and standout safety. Identification of bioactive peptides de novo using molecular docking is a widely used approach. However, current scoring functions are poorly optimized for peptide ligands. In this work, we present a novel algorithm PeptoGrid that rescores poses predicted by AutoDock Vina according to frequency information of ligand atoms with particular properties appearing at different positions in the target protein's ligand binding site. We explored the relevance of PeptoGrid ranking with a virtual screening of peptide libraries using angiotensin-converting enzyme and GABAB receptor as targets. A reasonable agreement between the computational and experimental data suggests that PeptoGrid is suitable for discovering functional leads.

SUBMITTER: Zalevsky AO

PROVIDER: S-EPMC6359344 | biostudies-literature | 2019 Jan

REPOSITORIES: biostudies-literature

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PeptoGrid-Rescoring Function for AutoDock Vina to Identify New Bioactive Molecules from Short Peptide Libraries.

Zalevsky Arthur O AO Zlobin Alexander S AS Gedzun Vasilina R VR Reshetnikov Roman V RV Lovat Maxim L ML Malyshev Anton V AV Doronin Igor I II Babkin Gennady A GA Golovin Andrey V AV

Molecules (Basel, Switzerland) 20190113 2

Peptides are promising drug candidates due to high specificity and standout safety. Identification of bioactive peptides de novo using molecular docking is a widely used approach. However, current scoring functions are poorly optimized for peptide ligands. In this work, we present a novel algorithm PeptoGrid that rescores poses predicted by AutoDock Vina according to frequency information of ligand atoms with particular properties appearing at different positions in the target protein's ligand b ...[more]

PMID: 30642123

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