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Hi developers of openmm-atm,
I was wondering if there was any available documentation / example code of how to run a RBFE for docked ligands against a PDB with a known co-cystal structure and groun…
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Hi,
Thanks for developing a great tool!
I was wondering:
1. What is the motivation for focusing only on predicting binding affinity (and presentation) to MHC Class I and not Class II?
- Is…
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### Week 1 - Get to know the community
- [X] Join the communication channels
- [X] Open a GitHub issue (this one!)
- [x] Install the Ersilia Model Hub and test the simplest model
- [x] Write a motiva…
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I would like to obtain the 2d protein representation for the 58 targets from your paper. Could you help me on how to do this?
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Hi,
I have pdb files of 2 molecules (an antibody and an antigen) predicted by Alphafold2-multimer.
Do I need to re-train RDE-PPI to run `pointmut_analysis.py`?
If I am not sure about the qual…
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Thanks for your great work!
I have set the Filtering Commands:
-b 500
-m median
--normal-cov 5
--normal-vaf 0.03
--tdna-cov 10
--tdna-vaf 0.05
but, the below result was in .all_epitopes.t…
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### Week 1 - Get to know the community
- [X] Join the communication channels
- [X] Open a GitHub issue (this one!)
- [X] Install the Ersilia Model Hub and test the simplest model
- [x] Write a motiva…
-
### Week 1 - Get to know the community
- [X] Join the communication channels
- [X] Open a GitHub issue (this one!)
- [x] Install the Ersilia Model Hub and test the simplest model
- [x] Write a motiva…
-
Hi All,
Can anybody give me some pointers to better underdstand FcRn kinetics in PK-Sim/Mobi?
Currently, I have the impression that no turnover of FcRn or degradation for the drug-FcRn complex is …
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### Model Name
Human Plasma Protein Binding (PPB) of Compounds
### Model Description
IDL-PPBopt aims at identifying the chemical substructures in small molecules that drive plasma protein bin…