-
**Is your feature request related to a problem? Please describe.**
Protein-ligand interactions may be complemented by interactions of the ligand with another ligand, which is located at the same bind…
-
Hi,
thank you for sharing your script of doing protein docking.
I am currently working with protein-protein interaction, and am trying to use your codes on my alphafold3 predicted structure.
Ho…
-
Hi there
Can explain what --pharma option does? I find --template option will bias docking toward pharmacophore defined in ph4 file. But I cannot find how --pharma option work. Any example can als…
-
## 🐛 Bug
This sample has many bugs, if you just try to run it, I want to propose the following fixes:
## To Reproduce
Steps to reproduce the behavior:
1. just try to run it and many exceptio…
-
## 🐛 Bug
**12 cell:**
%%time
max_epochs = 50
metric = dc.metrics.Metric(dc.metrics.score_function.rms_score)
step_cutoff = len(train)//12
def val_cb(model, step):
if step%step_cutoff!=0…
-
I am running AToM for ABFE for my systems. I adapted the control script from the tutorial and I am trying it on different ligands (more than 20 heavy atoms) bound to the same protein. For some of them…
-
Hello,
I really enjoyed the paper and am trying to implement this method to score several novel protein-ligand interactions that are not part of the training data. I have trained the model and am n…
-
Dear Omnipath team,
I would like to know if it is currently possible to access all data in Omnipath using the Cytoscape plugin?
Or will it miss certain interactions when compared to OmnipathR and py…
-
Hi. I have a receptor-ligand complex and I'm trying to generate plots to visualize the various types of interactions between the receptor and ligand proteins. The complex has 166 residues in total wit…
-
what is the PDB file format in oddt(RSC PDB, charmm PDB)?
I want to calculate interactions (salt bridge, hydrogen bonds, etc ) between a protein and a short peptide which obtained from MD simulation…