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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 a 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, s.~619-626. ISBN~978-1-4503-8713-2. Dostupné z: https://dx.doi.org/10.1145/3477314.3506988.
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