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FoldX Interface ΔΔG Calculation

Calculate protein interface ΔΔG values for a collection of proteins complexes given a list of mutations of interest for each complex. FoldX's AnalyseComplex command is run on each WT complex, then the required mutated models are predicted with BuildModel and analysed again with AnalyseComplex to determine the difference in binding strength.

Requirements

  • FoldX 5
  • Python 3
  • Snakemake
  • Numpy
  • Pandas

Usage

  1. Clone this repo
  2. Place your complex model PDB files as data/complex/{complex id}/model.pdb
  3. Add an individual_list file to each complex directory, as specified by FoldX's BuildModel
  4. Run Snakemake

Modifications

A number of simple modifications can be easily made:

  • Generate all possible interface mutants based on the output of the WT interface analysis (see my Mutfunc: SARS-CoV-2 pipeline)
  • Increase RAM requirements for individual complexes (see get_mut_complex_ram in Snakefile)
  • Analyse interfaces other than between chain A and B (see get_complex_tsv_files in Snakefile)