This repository contains the scripts needed for reproducing the results of Rapid and Sensitive Protein Complex Alignment with Foldseek-Multimer by Kim et al. 2024.
The following script downloads files from Zenodo, organizes them and unites those of them that had to be split due to file size limitations:
foldseek-multimer-analysis/datasets/download.sh
mkdir foldseek-multimer-analysis/datasets/CRISPR/PDBs
Download CIF files from wwpdb.org and put them in foldseek-multimer-analysis/datasets/CRISPR/PDBs
foldseek-multimer-analysis/datasets/remove.sh
foldseek-multimer-analysis/similar_pairs_benchmark/run_FS-MM_similar_pairs_benchmark.sh [Foldseek PATH] [TEMP DIR]
foldseek-multimer-analysis/similar_pairs_benchmark/run_US-align_similar_pairs_benchmark.sh [US-align PATH] [TEMP DIR]
foldseek-multimer-analysis/similar_pairs_benchmark/tot.py [TEMP DIR] [RESULT TSV]
foldseek-multimer-analysis/CRISPR_benchmark/run_CRISPR_createdb.sh [FOLDSEEK PATH] [THREADS] [DIR for DATABASE FILES]
foldseek-multimer-analysis/CRISPR_benchmark/run_CRISPR_benchmark.sh [FOLDSEEK PATH] [DIR for DATABASE FILES] [TEMP DIR]
foldseek-multimer-analysis/CRISPR_benchmark/run_US-align_CRISPR_runtime.sh [US-align PATH] [TEMP DIR] [OUTPUT FILE]
foldseek-multimer-analysis/CRISPR_benchmark/run_US-align_CRISPR_whole.sh [US-align PATH] [TEMP DIR] [OUTPUT PATH] [THREADS]
foldseek-multimer-analysis/3DComplexV7_benchmark/run_3DComplexV7_createdb.sh [FOLDSEEK PATH] [THREADS] [DIR for DATABASE FILES]
foldseek-multimer-analysis/3DComplexV7_benchmark/run_database_search.sh [US-align PATH] [FOLDSEEK PATH] [DIR for DATABASE FILES] [TSV OUTPUT PATH] [TEMP DIR]
foldseek-multimer-analysis/3DComplexV7_benchmark/run_FS-MM_3DComplexV7_benchmark.sh [FOLDSEEK PATH] [DIR for DATABASE FILES] [CSV OUTPUT] [THREADS] [TEMP DIR]
foldseek-multimer-analysis/3DComplexV7_benchmark/tot.py foldseek-multimer-analysis/datasets/3DComplexV7/QSalign_pairs.csv [CSV INPUT] [TSV OUTPUT PATH]