There are several docking applications and online tools available for docking (I am interested in protein-ligand docking). It would be very helpful if someone can recommend which of the open-source tools can be used for docking and MD simulation.
Ravi Ramalingam Hope you doing well
There is many software and server available for molecular docking like autodock tool, VINA pyrx etc. and for MD NAMD, Gromacs.
You can use MolAICal (https://molaical.github.io/MolDocking.html) for molecular docking that improves based on Autodock vina.
Then, you can use NAMD for MD simulation (https://www.ks.uiuc.edu/Research/namd). The MM/GBSA for assessing binding affinity can also be calculated by NAMD and MolAICal (https://molaical.github.io/).
Best,
Qifeng
I think you can use Autodock tools, because is free, and you can Manupulate. Unlike A. Vina
you could use pyrx for screening the ligands if you are having more number of ligands, where pyrx performs docking using auto dock vina.
further you could screen the results and go for a confirmatory docking using either auto dock vina or auto dock which ever you are comfortable with.
also if you are a command line user you could get perl pipelines which helps in automation of docking via auto dock vina if you are having more ligands.
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