I want to perform analyses on set of pdb files co-complexed with small ligands. I do not want to perform active site detection for small molecules but rather I want to concentrate on the change in the volume of the site occupied by the bound ligand.
Is there a tool which can help analyses of ligand pockets from trajectory. I tried mdpocket but no luck. TRAPP is a good tool but have difficulty uploading the trajectory files.
Hi Neha. I don't know if there is a tool that will do exactly what you require, but I'm certain snapshots from the MD run can be overlaid and a grid-based approach can easily be written up in Python to measure approximate volumes using a simple van der Waal's approach. I have done similar calculations in the past and can help if you would like. Just let me know.
- Aurijit
(asarkar1 at highpoint dot edu)
Hello ma'am,
I guess the following tool might help you:
http://nbcr.ucsd.edu/data/sw/hosted/POVME/
Hi Neha
I believe fpocket can do this for you
http://bioserv.rpbs.univ-paris-diderot.fr/services/fpocket
Good luck
Dan
Hi
You can use trj_cavity command. its an add on program.
download from here: https://sourceforge.net/projects/trjcavity/
Hi Neha,
Did you find a suitable tool to calculate the volume of a pocket over time (MD simulation)? At the end which tool did you use? I need some help, please.
Hi Neha,
CASTp would be helpful, free, and easy to use: http://sts.bioe.uic.edu/castp
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