ProteinMPNN (latest code on Oct 25, 2023)
Webpage
https://github.com/dauparas/ProteinMPNN
Version
latest code on Oct 25, 2023
Installation
ProteinMPNN
$ git clone https://github.com/dauparas/ProteinMPNN.git 20231025
python env (miniforge)
$ sh Miniforge3-Linux-x86_64.sh
...
[...] >>> /apl/ProteinMPNN/20231025/miniforge3
...
$ ./miniforge3/bin/conda shell.csh hook > conda_init.csh
$ ./miniforge3/bin/conda shell.bash hook > conda_init.sh
$ . conda_init.sh
$ conda install cudatoolkit=11.7.1 pytorch==1.13.1 torchvision==0.14.1 torchaudio==0.13.1 pytorch-cuda=11.7 -c pytorch -c nvidia
Mar 27, 2024: additional package for LigandMPNN
$ conda install prody pyparsing==3.1.1
Notes
- please see notes of RFdiffusion.
- LigandMPNN has problem with pyparsing 3.1.2