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.

Exploring the Mechanisms of Lian Hua Qing Wen Capsule against COVID-19 by Network Pharmacology and Molecular Docking Approach

“…PubChem and PDB were used to nd the chemical and conformational information of the relevant proteins and small-molecule compounds [16,17]. The AutoTools software was used to remove the redundant protein chains, ligands and water molecules with hydrogenation before running docking experiments [18]. The AutoGrid software was used to calculate the energy lattice points with the grid box coordinates of 15 × 15 × 15 [18].…”

“…The AutoTools software was used to remove the redundant protein chains, ligands and water molecules with hydrogenation before running docking experiments [18]. The AutoGrid software was used to calculate the energy lattice points with the grid box coordinates of 15 × 15 × 15 [18]. AutoDock Vina was used to simulate the docking condition between proteins and small molecules [18].…”

“…The AutoGrid software was used to calculate the energy lattice points with the grid box coordinates of 15 × 15 × 15 [18]. AutoDock Vina was used to simulate the docking condition between proteins and small molecules [18]. The Schrodinger software was used to analyse the preferential conformation and map the simulation.…”

“…Discovery Studio software [18] was used to validate network pharmacology by molecular docking, including the respective top 5 targets in PPI network and the top 5 compounds in LHQW capsule. The LibDock score represented the degree of docking coincidence of molecules.…”

Computational Approaches for Drug Discovery

“…A reasonable agreement between the computational and experimental data suggests that PeptoGrid is suitable for discovering functional leads. The PeptoGrid software is available at [34].…”