Po-Yu Kao

Training Configuration of pre-trained MPNN_CNN

12

Hi Kexin Huang, I am using the provided pre-trained MPNN_CNN model. When I looked into its model configuration file, it looks wired to me. {'input_dim_drug': 1024, 'input_dim_protein': 8420, 'hidden_dim_drug': 128,...

1. Export conda environment into `experiment.yml` file. 2. `.gitignore` ignore logs. 3. `run_all_experiments.sh` run all experiments in MolTrans paper. 4. changed hyperparameters in `train.py` to match MolTrans paper.

1. Changed `pytest .` to `python -m pytest .` 2. Changed python version from 3.6 to 3.7 and added the required libraries. 3. Have run the test code, and the...

Model gives different scores for the same drug-target pairs

4

Hi Kexin, I tried to write the inference code to predict the binding affinity probability given the drug-target pairs. However, I found that the `model` always gives different `scores` for...

add one more space to pass the codestyle issue

added data location

Hi Qin, Great work! Do you have the environment file of conda for running your code? Best, Ken

Hello, This is an amazing work. I am trying to test DiffDock using a simple example 7A1L with the following commands: ``` python -m inference --protein_sequence MAATAAEAVASGSGEPREEAGALGPAWDESQLRSYSFPTRPIPRLSQSDPRAEELIENEEPVVLTDTNLVYPALKWDLEYLQENIGNGDFSVYSASTHKFLYYDEKKMANFQNFKPRSNREEMKFHEFVEKLQDIQQRGGEERLYLQQTLNDTVGRKIVMDFLGFNWNWINKQQGKRGWGQLTSNLLLIGMEGNVTPAHYDEQQNFFAQIKGYKRCILFPPDQFECLYPYPVHHPCDRQSQVDFDNPDYERFPNFQNVVGYETVVGPGDVLYIPMYWWHHIESLLNGGITITVNFWYKGAPTPKRIEYPLKAHQKVAIMRNIEKMLGEALGNPQEVGPLLNTMIKGRYN --ligand "C[C@@H](CC(=O)O)C(=O)C(=O)O" --out_dir...

Python restrict