Po-Yu Kao

Actually, I ran the same FASTA sequence twice using the same setting, and AF give me different results (fragments aligned: 74%) for O00141.

Dear all, I probably find the reason why the resulting structures are different: https://github.com/deepmind/alphafold/blob/b85ffe10799ca08cc62146f1dabb4e4ee6c0a580/run_alphafold.py#L105-L109

Hi @mrinal-shekhar, I got the same error when I was trying to call `python multiligand_inference.py` ``` DGL backend not selected or invalid. Assuming PyTorch for now. Setting the default backend...

@niksubramanian I am using CUDA11.7. I will try to modify the `environment.yml` file to make it work with CUDA11.7. Thanks, Ken

Thank you for pointing out the issue and providing the solution. I also face the same issue here: the dimension of generated single representation is larger than the length of...

Did you use the latest BindingDB to train this model?

Thank you for your reply 👍🏽 Please let me know if you want the trained MPNN_CNN on BindingDB using Kd.

Hi @TWRogers , I tried to reproduce the QSAR tasks using the script `scripts/run_qsar_test_molbert.py` but I find it is hard to run CDDD and MolBert in the same script. MolBert...

@TWRogers , I also get poor predictions compared to the MolBert paper. Fine-tuned MolBert sometimes gets worse performance than MolBert without any fine-tuning. Maybe we need to get the details...

Hi, I am facing the same issue. I am not able to use the fine-tuned model to generate fine-tuned MolBert features. I have tried 1. manually append `named_descriptor_set: all` in...