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@inproceedings{1853582,
author = {Němcová, Petra and Hozzová, Jana and Filipovič, Jiří},
address = {USA},
booktitle = {SAC '22: Proceedings of the 37th ACM/SIGAPP Symposium on Applied Computing},
doi = {http://dx.doi.org/10.1145/3477314.3506988},
keywords = {CaverDock; ligand transport; flexible receptor; molecular docking; search heuristic; continuous space search},
howpublished = {elektronická verze "online"},
language = {eng},
location = {USA},
isbn = {978-1-4503-8713-2},
pages = {619-626},
publisher = {Association for Computing Machinery},
title = {Improving ligand transport trajectory within flexible receptor in CaverDock},
url = {https://dl.acm.org/doi/10.1145/3477314.3506988},
year = {2022}
}
TY - JOUR
ID - 1853582
AU - Němcová, Petra - Hozzová, Jana - Filipovič, Jiří
PY - 2022
TI - Improving ligand transport trajectory within flexible receptor in CaverDock
PB - Association for Computing Machinery
CY - USA
SN - 9781450387132
KW - CaverDock
KW - ligand transport
KW - flexible receptor
KW - molecular docking
KW - search heuristic
KW - continuous space search
UR - https://dl.acm.org/doi/10.1145/3477314.3506988
N2 - 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.
ER -
NĚMCOVÁ, Petra, Jana HOZZOVÁ and Jiří FILIPOVIČ. Improving ligand transport trajectory within flexible receptor in CaverDock. Online. In \textit{SAC '22: Proceedings of the 37th ACM/SIGAPP Symposium on Applied Computing}. USA: Association for Computing Machinery, 2022, p.~619-626. ISBN~978-1-4503-8713-2. Available from: https://dx.doi.org/10.1145/3477314.3506988.
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