foldmason-analysis

File	Description
clean_homstrad.py	Clean Homstrad family folders, generate individual PDB files, AA FASTA files, Homstrad MSA
download_homstrad.sh	Downloads latest Homstrad database from FTP, unpacks and fixes igV family
compute_scores.sh	Compute SoP (forward and backward), TC and CS scores (Homstrad), extract LDDT and runtime
extractLDDT.awk	Extract LDDT scores from msa2lddt HTML report
align_family.sh	Run tools on a given folder and generate msa2lddt reports on each resulting MSA
align_families.sh	Run tools on all subdirectories of given folder and compute LDDT scores (+SP/TC/CS if Homstrad MSA found)

Instructions

Prerequisites

Ensure the following tools are available on system $PATH:

foldmason
caretta-cli
muscle (version 5)
famsa (version 2)
mafft (linsi mode)
clustalo
Matt
mustang
mTM-align
t_coffee (for computing SoP/TC/CS scores)

Also that the directory structure of the dataset resembles:

folder/
    family1/
        pdbs/
            structure1.pdb
            structure2.pdb
            structure3.pdb
            ...
        family1_msa.fa (Homstrad reference alignment)
        family1_aa.fa
    family2/
        ...
    ...

Process

1. Run download_homstrad.sh to download latest Homstrad release and prepare it for analysis. Generates directories homstrad_db (raw) and homstrad_clean (processed).
2. Run ./align_families.sh homstrad_clean homstrad_scores.tsv to run the full suite of tools on the Homstrad database, and save all scores and runtimes to homstrad_scores.tsv.