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Simulation of Ligand Transport in Receptors Using CaverDock
J. Hozzová, O. Vávra, D. Bednář, J. Filipovič
Language English Country United States
Document type Journal Article, Research Support, Non-U.S. Gov't
- MeSH
- Chlorohydrins chemistry MeSH
- Ethanol analogs & derivatives chemistry MeSH
- Ethylene Dibromide chemistry MeSH
- Hydrolases chemistry MeSH
- Arachidonic Acid chemistry MeSH
- Ligands MeSH
- Drug Discovery methods MeSH
- Proteins chemistry MeSH
- Drug Design MeSH
- Molecular Dynamics Simulation MeSH
- Molecular Docking Simulation methods MeSH
- Software MeSH
- Cytochrome P-450 Enzyme System chemistry MeSH
- Thermodynamics MeSH
- Protein Binding MeSH
- Binding Sites MeSH
- Structure-Activity Relationship MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
Interactions between enzymes and small molecules lie in the center of many fundamental biochemical processes. Their analysis using molecular dynamics simulations have high computational demands, geometric approaches fail to consider chemical forces, and molecular docking offers only static information. Recently, we proposed to combine molecular docking and geometric approaches in an application called CaverDock. CaverDock is discretizing enzyme tunnel into discs, iteratively docking with restraints into one disc after another and searching for a trajectory of the ligand passing through the tunnel. Here, we focus on the practical side of its usage describing the whole method: from getting the application, and processing the data through a workflow, to interpreting the results. Moreover, we shared the best practices, recommended how to solve the most common issues, and demonstrated its application on three use cases.
References provided by Crossref.org
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