Design - polizzilab/software-wiki GitHub Wiki

Combs2

workstation installation path: /nfs/polizzi/shared/programs/design/Combs2/
o2 installation path: /n/data1/hms/bcmp/polizzi/lab/Combs2/

github: https://github.com/npolizzi/Combs2 (Note: the most up-to-date branch is called combs2prop)

pulled and maintained by: jchang, jmou, npolizzi

last date pulled: 08/05/23

A general overview of the algorithm can be found in this google doc
Brief tutorials on how to run combs can be found in the repo under tutorials/:
- A brief explanation of the steps are in this notebook
- An example python script to run combs with biotin is here
Various lab members have written scripts which use Combs for design:
- Jody has made a detailed explanation of the full design workflow is illustrated with the ligand doxorubicin in the repo polizzilab/doxo
- Jerry has scripts to run a parameter sweep of combs here. Note that this is with a fixed ligand placement!

workstation installation path: /nfs/polizzi/shared/programs/design/RFdiffusion/

pulled and maintained by: jmou

last date pulled: 4/01/23

if you don't want to install the environment yourself, you can use /nfs/polizzi/jmou/miniconda3/envs/SEnv - I also added prody to this environment
see github and example scripts at https://github.com/RosettaCommons/RFdiffusion/tree/main/examples
RFdiffusion uses hydra to parse inputs. The full set of available options are in the config file here.
using the inpaint_seq option generally has given lower quality results, i.e. backbone irregularities and larger backbone deviation from the fixed structure

workstation installation path: /nfs/polizzi/shared/programs/design/ProteinMPNN/

pulled and maintained by: jmou

last date pulled: 3/24/23

the github readme provide a reasonable introduction
a number of example scripts can be found in /nfs/polizzi/shared/programs/design/ProteinMPNN/examples/
a full list of run settings can be found in the argparse descriptions of protein_mpnn_run.py
helper scripts are uploaded here:
- run_mpnn.sh
  - example run script for the workstation (adapted from example scripts)
- get_unique_seqs.py
  - extract and deduplicate sequence outputs and scores into a dataframe
  - run using python get_unique_seqs.py -i path/to/fasta.fa -o path/to/output/
- outputs.ipynb
  - jupyter notebook to analyze proteinMPNN outputs by making sequence logos, plotting the probabilities and scores

workstation installation path: /nfs/polizzi/shared/programs/design/AttnPacker

pulled and maintained by: jchang

last date pulled: 11/13/23

see the readme file at /nfs/polizzi/shared/programs/design/AttnPacker/README_polizzi

workstation installation path: /nfs/polizzi/shared/miniconda3/envs/evcouplings/

pulled and maintained by: jchang

last date pulled: 02/01/2024

do conda activate /nfs/polizzi/shared/miniconda3/envs/evcouplings/

(I installed this by making a new conda environment, installing pip, and then running pip install of the latest development version .zip)