Improving ligand transport trajectory within flexible receptor in CaverDock
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14610%2F22%3A00125815" target="_blank" >RIV/00216224:14610/22:00125815 - isvavai.cz</a>
Result on the web
<a href="http://dx.doi.org/10.1145/3477314.3506988" target="_blank" >http://dx.doi.org/10.1145/3477314.3506988</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1145/3477314.3506988" target="_blank" >10.1145/3477314.3506988</a>
Alternative languages
Result language
angličtina
Original language name
Improving ligand transport trajectory within flexible receptor in CaverDock
Original language description
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.
Czech name
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Czech description
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Classification
Type
D - Article in proceedings
CEP classification
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OECD FORD branch
10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)
Result continuities
Project
<a href="/en/project/LM2018140" target="_blank" >LM2018140: e-Infrastructure CZ</a><br>
Continuities
P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)
Others
Publication year
2022
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Article name in the collection
SAC '22: Proceedings of the 37th ACM/SIGAPP Symposium on Applied Computing
ISBN
9781450387132
ISSN
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e-ISSN
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Number of pages
8
Pages from-to
619-626
Publisher name
Association for Computing Machinery
Place of publication
USA
Event location
Brno, CZ
Event date
Jan 1, 2022
Type of event by nationality
WRD - Celosvětová akce
UT code for WoS article
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