This repo documents the code used to carry out the analysis for the paper titled: 'AlphaFold reveals how pathogenic Leptospira use cross-kingdom thiol-disulphide exchange to evade the complement membrane attack complex'.
Analysis was carried out on the Barkla1 cluster, using GPU acceleration for model generation. It should be fully reproducible starting from two fasta files: 'LIC13259_sequences_no_his_tag.fasta' and 'c8_uniprotkb_2024_07_25.fasta' contained within the raw_fasta folder.
In addition to this, the analysis requires three key pieces of software to be installed (in addition to a standard Rstudio set-up):
- ColabFold installation instructions can be found here
- FoldSeek installation instructions and tutorials can be found here
- Alphapulldown installation instructions and tutorials
The analysis was primarily carried out using a series of bash scripts and quarto markdown documents (qmds). These should be run in order. Supporting scripts are found inside the scripts folder, these are a mixture of python (version 3.10) and R (4.2) scripts.