Comments (4)
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.
from protocaller.
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 .
from protocaller.
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.
from protocaller.
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 resultingBioSimSpace
objects, and even manipulate them further withinBioSimSpace
if you need to.
thanks, I will try.
from protocaller.
Related Issues (20)
- Abnormal memory usage in protocaller HOT 13
- The merge has opened/closed a ring HOT 12
- An input file contains a line longer than 4095 characters HOT 4
- LINCS warning and structure clash HOT 7
- Can I supply a ligand coordinate file as input? HOT 1
- H bond constraint HOT 1
- How to supply a custom pdb file (without pdb id) for protein? HOT 2
- Memory usage constantly growing with the number of perturbations. HOT 6
- How to restore ligand from parametrised file? HOT 2
- Select chain from polymer HOT 5
- Molecule ID not found HOT 1
- Explicit valence for atom # 37 C greater than permitted HOT 5
- Error while calling command 'antechamber' HOT 1
- minimise not take effect when protonated was set to True HOT 2
- Invalid file format for file HOT 2
- tleap failed for protein HOT 2
- Not all chains are contained in the FASTA sequence
- Installing error
- running error
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