OpenFold https://github.com/aqlaboratory/openfold is a “faithful but trainable PyTorch reproduction of DeepMind’s Alphafold2”. It is a tool for predicting protein structures. OpenFold is now available as an experimental module. To install a local copy for yourself, please see Installing OpenFold Locally on O2.
Compared to AlphaFold (Using AlphaFold on O2) OpenFold takes about the same amount of parameters, and can use either jackhmmer or mmseqs2 for the multiple sequence alignment (MSA) step of analysis. OpenFold is generally faster than AlphaFold (up to 2x) and adept at processing extremely long chains (4000+ residues).
...
| Code Block |
|---|
>header1 COMPLEXPROTIENSEQUENCE1 >header2 COMPLEXPROTIENSEQUENCE2 >header3 COMPLEXPROTIENSEQUENCE3 >header4 COMPLEXPROTIENSEQUENCE4 |
Generating MSAs with
...
Jackhmmer or MMSeqs2 using OpenFold Scripts
OpenFold presents 2 options for generating MSAs, below we will adapt the code presented in the readme to O2. The first example is using jackhmmer. Note that this script outputs help information by running:
...
This script should generate a series of files in the output dir, including the msa files. The second method uses mmseqs2 to generate the MSA. Similar to the JackHMMER jackhmmer method, we can get help information by running:
...