Antoine Lacour

Training scoring functions and updated version of PDBBind

2

I am currently trying to train the NNScore and PLECScore models for ligand scoring. So far I have not found a way to train the model "purposefully" and have resorted...

GNINA generating incorrect bond orders

3

### Issue summary I've been using GNINA and for some compounds in my test set, the bond orders are generated incorrectly, leading to errors when parsing the SDF output using...

[QUESTION]: Basic MolPal usage

4

First of all, I would like to thank you for your work with MolPal, I'm sure this will be very useful to the drug discovery community in the future. I...

Hi, I've been trying to run pka solver (calculate microstates function) on a fairly large dataset of compounds (>1000). Unfortunately, it seems the function simply stops running after a while....

Question regarding (new?) metropolis scoring schemes

1

### Issue summary I noticed some additional --cnn_scoring arguments have been added (or at least I don't remember them being in previous releases). These are metrorescore, (metropolis+rescore) and metrorefine (metropolis+refine)....

Streamlit Integration

1

Hi, I was wondering if there was any way of integration molplotly into a streamlit app. This is some very code I have : ``` fig = visualize_chemical_space(library_to_visualise, method, fingerprint)...

Thanks a lot for the work done here. I am trying to generate .pdbqt files using Meeko (https://github.com/forlilab/Meeko) and was recommended to use PDB2PQR to parse the PDB files before...

Python 3.10 compatibility?

1

Hi, Thanks a lot for the work done here, I was wondering if there were any plans to update the package to python 3.10 and over? Cheers, Tony

# DockM8 Feature Request ## Description Add ability to generate protein conformational ensemble automatically to then use in ensemble docking. ## Problem Statement Several conformations may not be available for...

IF-SitePred : [github](https://github.com/oxpig/binding-sites) P2Rank : [github](https://github.com/rdk/p2rank)