Jin Su
Hi, Apology for the late reply! I've been busy working on another project and didn't see the new issue:( > Is there a way which does not use .mdb for...
Hi, thank you for you interest in our work! The ProteinGym benchmark is actually its 1.0 version. The ProteinGym dataset used in our paper is the 0.1 version, which was...
Hi, Yes. Because only partial protein structures in AlphaFoldDB have corresponding PDB entries. We filtered out all proteins without PDB entries.
Hi, Both amino acid sequence and foldseek sequence are obtained by using ``foldseek`` binary file. Sometimes ``foldseek`` parses extra amino acids given a pdb file. Maybe you could check the...
Hi JQ, Have you installed the environment successfully before running the script ``run.sh``?
Maybe you should first go into the ``local_server`` directory? The system assumes you are in this directory and finds files using relative path.
Can you run the installation from scratch in the ``local_server`` directory? Also, it looks like the jupyter notebook runs normally as expected. 
Hi, You also have to change the cache directory in ``jupyter_notebook_config.py`` and then everything should be OK。
And then you can follow the instructions to connect to you local server as here: 
Is your server remote? If your server is a remote server, you have to follow the optional step and then input identically as the instruction does.