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protocaller / ProtoCaller

Full automation of relative protein-ligand binding free energy calculations in GROMACS
http://protocaller.readthedocs.io
GNU General Public License v3.0
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Can I use ProtoCaller in protein-protein system? #24

Closed meetxinzhang closed 3 years ago

msuruzhon commented 3 years ago

Hi,

ProtoCaller can only deal with ligand-ligand perturbations. If we are talking about a protein-protein system and you are interested in a ligand perturbation in one of them, then this should be possible with some tweaking - simply create two separate Ensemble systems and after you perform parametrisation and alignment on both of them, you can combine the resulting BioSimSpace objects, and even manipulate them further within BioSimSpace if you need to.

kexul commented 3 years ago

If you are talking about protein-protein mutation, here is a nice tutorial using biobb. https://biobb-wf-pmx-tutorial.readthedocs.io/en/latest/tutorial.html @MeetDevin .

meetxinzhang commented 3 years ago

If you are talking about protein-protein mutation, here is a nice tutorial using biobb. https://biobb-wf-pmx-tutorial.readthedocs.io/en/latest/tutorial.html @MeetDevin .

thanks, biobb is particularly useful for my work.

meetxinzhang commented 3 years ago

If you are talking about protein-protein mutation, here is a nice tutorial using biobb. https://biobb-wf-pmx-tutorial.readthedocs.io/en/latest/tutorial.html @MeetDevin .

thanks, biobb is particularly useful for my work

Hi,

ProtoCaller can only deal with ligand-ligand perturbations. If we are talking about a protein-protein system and you are interested in a ligand perturbation in one of them, then this should be possible with some tweaking - simply create two separate Ensemble systems and after you perform parametrisation and alignment on both of them, you can combine the resulting BioSimSpace objects, and even manipulate them further within BioSimSpace if you need to.

thanks, I will try.