Improving ligand transport trajectory within flexible receptor in CaverDock

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Publikace nespadá pod Ekonomicko-správní fakultu, ale pod Ústav výpočetní techniky. Oficiální stránka publikace je na webu muni.cz.
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NĚMCOVÁ Petra HOZZOVÁ Jana FILIPOVIČ Jiří

Rok publikování 2022
Druh Článek ve sborníku
Konference SAC '22: Proceedings of the 37th ACM/SIGAPP Symposium on Applied Computing
Fakulta / Pracoviště MU

Ústav výpočetní techniky

Citace
www https://dl.acm.org/doi/10.1145/3477314.3506988
Doi http://dx.doi.org/10.1145/3477314.3506988
Klíčová slova CaverDock; ligand transport; flexible receptor; molecular docking; search heuristic; continuous space search
Popis The receptor-ligand interactions are an important part of many biologically relevant processes. The small ligand molecule needs to pass via a tunnel into a receptor before the interaction of interest begins. Both receptor-ligand interaction and ligand pathway need to be studied. CaverDock is a computational tool that simulates the transport of the ligand in a tunnel. However, in its first version, CaverDock allowed only limited flexibility of the receptor, biasing the measured energy of ligand transportation. In this paper, we introduce two essential extensions to CaverDock. First, we combine its force field with AMBER, which allows to relax receptor’s geometry in tunnel bottlenecks. Second, we improve CaverDock heuristics for ligand trajectory search to obtain multiple variants of ligand trajectories, ideally with lower energy compared to the result of CaverDock 1.0. We experimentally demonstrate that the new heuristic is superior to the original one and that the receptor relaxation improves precision of CaverDock results.
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