foldseek-multimer-analysis

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.

Obtaining Datasets

Download

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

Remove

foldseek-multimer-analysis/datasets/remove.sh

Similar Pairs Benchmark

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-MM

foldseek-multimer-analysis/pairwise_benchmark/run_foldseek-MM_similar_pairs.sh [FOLDSEEK PATH] [OUTPUT PATH]

Foldseek-MM-TM

foldseek-multimer-analysis/pairwise_benchmark/run_foldseek-MM-TM_similar_pairs.sh [FOLDSEEK PATH] [OUTPUT PATH]

US-align

foldseek-multimer-analysis/pairwise_benchmark/run_US-align_similar_pairs.sh [US-align PATH] [OUTPUT PATH]

US-align-fast

foldseek-multimer-analysis/pairwise_benchmark/run_US-align-fast_similar_pairs.sh [US-align PATH] [OUTPUT PATH]

CRISPR Benchmark

Createdb

foldseek-multimer-analysis/3DComplexV7_benchmark/run_CRISPR_createdb.sh [FOLDSEEK PATH] [threads]

Foldseek-MM

foldseek-multimer-analysis/CRISPR_benchmark/run_foldseek-MM_CRISPR.sh [FOLDSEEK PATH] [OUTPUT PATH]

Foldseek-MM-TM

foldseek-multimer-analysis/CRISPR_benchmark/run_foldseek-MM-TM_CRISPR.sh [FOLDSEEK PATH] [OUTPUT PATH]

US-align: runtime with 1,000 targets

foldseek-multimer-analysis/CRISPR_benchmark/run_US-align_CRISPR_runtime.sh [US-align PATH] [OUTPUT PATH]

US-align: all positive results

foldseek-multimer-analysis/CRISPR_benchmark/run_US-align_CRISPR_whole.sh [US-align PATH] [OUTPUT PATH] [threads]

3DComplexV7 Benchmark

Createdb

foldseek-multimer-analysis/3DComplexV7_benchmark/run_3DComplexV7_createdb.sh [FOLDSEEK PATH] [threads]

Runtime

foldseek-multimer-analysis/3DComplexV7_benchmark/run_3DComplexV7_runtime.sh [US-align PATH] [FOLDSEEK PATH] [OUTPUT PATH]

Foldseek-MM

foldseek-multimer-analysis/3DComplexV7_benchmark/run_3DComplexV7_benchmark.sh [FOLDSEEK PATH] [CSV OUTPUT PATH] [threads]

Figures [With your Data]

foldseek-multimer-analysis/pairwise_benchmark/fig.py foldseek-multimer-analysis/datasets/3DComplexV7/QSalign_pairs.csv [CSV PATH] [FIGURE(PNG) OUTPUT PATH]

Figures [With Ready-made Data]

foldseek-multimer-analysis/pairwise_benchmark/fig.py foldseek-multimer-analysis/datasets/3DComplexV7/QSalign_pairs.csv foldseek-multimer-analysis/datasets/3DComplexV7/FS-MM.csv [FIGURE(PNG) OUTPUT PATH]