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 PDB files from wwpdb.org and put them in foldseek-multimer-analysis/datasets/CRISPR/PDBs
foldseek-multimer-analysis/datasets/remove.sh
foldseek-multimer-analysis/pairwise_benchmark/run_similar_pairs_benchmark.sh [US-align PATH] [FOLDSEEK PATH] [TSV OUTPUT PATH]
foldseek-multimer-analysis/pairwise_benchmark/fig.py [TSV OUTPUT PATH] [FIGURE(PNG) OUTPUT PATH]
foldseek-multimer-analysis/pairwise_benchmark/run_foldseek-MM_similar_pairs.sh [FOLDSEEK PATH] [OUTPUT PATH]
foldseek-multimer-analysis/pairwise_benchmark/run_foldseek-MM-TM_similar_pairs.sh [FOLDSEEK PATH] [OUTPUT PATH]
foldseek-multimer-analysis/pairwise_benchmark/run_US-align_similar_pairs.sh [US-align PATH] [OUTPUT PATH]
foldseek-multimer-analysis/pairwise_benchmark/run_US-align-fast_similar_pairs.sh [US-align PATH] [OUTPUT PATH]
foldseek-multimer-analysis/CRISPR_benchmark/run_CRISPR_createdb.sh [FOLDSEEK PATH] [threads]
foldseek-multimer-analysis/CRISPR_benchmark/run_foldseek-MM_CRISPR.sh [FOLDSEEK PATH] [OUTPUT PATH]
foldseek-multimer-analysis/CRISPR_benchmark/run_foldseek-MM-TM_CRISPR.sh [FOLDSEEK PATH] [OUTPUT PATH]
foldseek-multimer-analysis/CRISPR_benchmark/run_US-align_CRISPR_runtime.sh [US-align PATH] [OUTPUT PATH]
foldseek-multimer-analysis/CRISPR_benchmark/run_US-align_CRISPR_whole.sh [US-align PATH] [OUTPUT PATH] [threads]
foldseek-multimer-analysis/3DComplexV7_benchmark/run_3DComplexV7_createdb.sh [FOLDSEEK PATH] [threads]
foldseek-multimer-analysis/3DComplexV7_benchmark/run_3DComplexV7_runtime.sh [US-align PATH] [FOLDSEEK PATH] [OUTPUT PATH]
foldseek-multimer-analysis/3DComplexV7_benchmark/run_3DComplexV7_benchmark.sh [FOLDSEEK PATH] [CSV OUTPUT PATH] [threads]
foldseek-multimer-analysis/3DComplexV7_benchmark/fig.py foldseek-multimer-analysis/datasets/3DComplexV7/QSalign_pairs.csv [CSV PATH] [FIGURE(PNG) OUTPUT PATH]
foldseek-multimer-analysis/3DComplexV7_benchmark/fig.py foldseek-multimer-analysis/datasets/3DComplexV7/QSalign_pairs.csv foldseek-multimer-analysis/datasets/3DComplexV7/FS-MM.csv [FIGURE(PNG) OUTPUT PATH]