Installing foldx

One of the main subset of black-boxes of poli relates to foldx, a suite for protein design that allows you to compute, among other things, the change in free energy \(ddG\). This software and metric have been used as a black-box for optimization in recent work [Jain et al., 2023, Stanton et al., 2022].

poli can’t install foldx for you automatically, since the software is provided under an academic license. To install foldx,

1. Go to https://foldxsuite.crg.eu/

2. Download the academic license. You’ll likely be downloading a zip file with the executable and auxiliary files.

3. Create a folder in your home directory called foldx.

4. Place your executable under ~/foldx/foldx. You will need to rename it.

5. (If you downloaded foldx version 4) Make sure you have the rotabase.txt at ~/foldx/rotabase.txt

If you installed everything correctly, you should be able to run

~/foldx/foldx --help

Warning

If you are using mac, it is likely that the operating system will raise a warning about foldx being an unverified executable. You can remove the quarantine with the following command:

# Use at your own risk! This removes the quarantine from foldx 
xattr -d com.apple.quarantine ~/foldx/foldx