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Molecules 2019, 24(2), 277; https://doi.org/10.3390/molecules24020277

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

1
Faculty of Bioengineering, Lomonosov Moscow State University, Moscow 119234, Russia
2
Ineractomics Lab, Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow 119146, Russia
3
Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia
4
Lactocore Inc., Plymouth, MI 48170, USA
5
Department of Human and Animal Physiology, Faculty of Biology, Lomonosov Moscow State University, Moscow 119899, Russia
6
Faculty of Computer Science, National Research University Higher School of Economics, Moscow 101000, Russia
*
Author to whom correspondence should be addressed.
Received: 26 November 2018 / Revised: 5 January 2019 / Accepted: 9 January 2019 / Published: 13 January 2019
(This article belongs to the Special Issue Computational Approaches for Drug Discovery)
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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. View Full-Text
Keywords: docking; peptides; rescoring; gabab receptor; Danio rerio docking; peptides; rescoring; gabab receptor; Danio rerio
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Zalevsky, A.O.; Zlobin, A.S.; Gedzun, V.R.; Reshetnikov, R.V.; Lovat, M.L.; Malyshev, A.V.; Doronin, I.I.; Babkin, G.A.; Golovin, A.V. PeptoGrid—Rescoring Function for AutoDock Vina to Identify New Bioactive Molecules from Short Peptide Libraries. Molecules 2019, 24, 277.

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