My name is Anne-Sophie Chys. I am a bioinformatics student from the Howest University of Applied Sciences in the year of 2023. I do my traineeship at the University Gent in the department of Biotechnology in the Biochemistry & Glycobiology Research group.
This traineeship aims to investigate the evolution of OsGH27-homologs in plants and to perform molecular docking of carbohydrates.
The dynamics of docking refers to the process of molecular docking that takes into account the movement and flexibility of the protein and ligand molecules involved. Traditional docking methods typically assume that the protein and ligand are rigid, but in reality, both molecules are flexible and can undergo conformational changes during the binding process.
Dynamic docking methods use molecular dynamics simulations to simulate the movements and interactions of the protein and ligand over time, taking into account their flexibility and changes in conformation. These simulations can provide more accurate predictions of binding affinities and binding modes than static docking methods.
In this case there are multiple dockings performed that needs to undergo dynamics for confirmation. This is done with a short bashscript where the dynamics will be performed automatically from directory to directory. A tree of the directories can be revieuwed below:
charmm* -> amber -> README
These 'charmm*' directories containing the amber and README files, are obtained from CHARMM-GUI. For this dynamics, there is chosen for the option 'Input Generator' to perform a 'Solution Builder'. The options to build these files are free to choose, only what is specific to this set of directories, is the choice of the 'Force Field Options:' and the 'Input Generation Options:' as 'AMBER'.