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ccsb-scripps / AutoDock-GPU

AutoDock for GPUs and other accelerators
https://ccsb.scripps.edu/autodock
GNU General Public License v2.0
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Is it good practice to remove bound proteins too? #242

Open syedzayyan opened 1 year ago

syedzayyan commented 1 year ago

I am using these structures

https://www.rcsb.org/structure/6D9H https://www.rcsb.org/structure/5N2S

And both of them contain bound things. 6D9H has a bound G - Protein, while 5N2S has a cytochrome attached. Is it necessary to remove them if we are drawing a binding box anyway?

diogomart commented 1 year ago

It depends on the system and on what you want to do. Reading about protein-protein interface inhibitors may (or may not) help you decide what to do.