A comprehensive toolkit for identifying, clustering, annotating, and visualizing protein-protein interaction (PPI) sites and residue clusters.
- Build a residue distance database from PDB/mmCIF structures
- Detect and cluster protein interaction sites
- Integrate multi-source functional annotations (mutation, PTM, pocket info, drug targets, etc.)
- Visualize cluster composition, distribution, and dynamics
- Analyze mutation frequency, PTM levels, and structural dynamics
- Python 3.x
- PostgreSQL (for residue distance database)
- R (for downstream analysis and visualization)
python build_res_distance_database.py \
--input-directory /path/to/database_pdb \
--csv-path /path/to/pdb_inf.txt \
--conn-string "dbname='xxx' user='xxx' password='xxx' host='localhost' port='5432'" \
--threshold 8.0 \
--workers 8Input: PDB/CIF files Output: Residue distance database
python cluster_sites.py \
--input-dir /path/to/sites_txt_new \
--output-dir /path/to/cluster_result_new \
--db-mon-conn "dbname='xxx' ..." \
--db-ppi-conn "dbname='xxx' ..."Output example: Cluster assignment, C(vi), Cc
Process_PPI_cluster_results.R → outputs Cluster_Raw.xlsx, Single_Site_Data_Raw.xlsx
Merge_cluster_with_annotations.R → integrates PDB info, BioLiP pockets, Fpocket, PTM, mutation, COSMIC, DrugBank, ASD, NACCESS
Plot_Cc_density.R → plots Cc distribution density
Plot_cluster_composition.R → pie charts of cluster composition/distribution
Plot_heatmap_mutation_PTM.R → mutation frequency & PTM heatmap- ANM calculation
python ppi_dynamic.py anm \
--pdb-dir /path/to/pdb \
--ppi-info /path/to/dynamic_calc_info.txt \
--out-singleAA /path/to/results/anm/singleAA_Data \
--out-cc /path/to/results/anm/CC_Matrix \
--out-prs /path/to/results/anm/PRS_MatrixVisualize_MD_results.R → visualization of ANM/GNM dynamics results