Protein-protein docking studies –Protein Docking Analysis of BRCA with human kallikreins for prostate cancerHuman Kallikreins in Prostate Cancer
Description
For our study on Protein-protein docking studies –Protein Docking Analysis of BRCA with human kallikreins for prostate cancerHuman Kallikreins in Prostate Cancer , the data includes all the docking files for recarrying out the experiment. Top-ranked docked PDB files for each receptor–ligand pair (.pdb) Scoring summaries (.txt or .csv) listing HDOCK scores and rank order Configuration files showing the input parameters used for each docking run A README in the dataset provides file descriptions and instructions for re-using the docking results.
Files
Steps to reproduce
1. Retrieve and Prepare Structures Download PDB files BRCA1 WT: PDB 3FA2 BRCA1 variants: use 3FA2 + in silico mutagenesis (see below) BRCA2 WT: PDB 1IYJ BRCA2 variants: use 1IYJ + in silico mutagenesis Human kallikreins: hK1 → 1SPJ hK2 → 5HEX hK3 (PSA) → 3HM8 hK4 → 2BDG Clean each PDB with Discovery Studio Visualizer v4.5 (Dassault Systèmes): Remove waters, ions, co‐crystallized ligands Add polar hydrogens at pH 7.4 (Protonate3D algorithm) Assign standard protonation states Save as Receptor_minimized_structures/BRCA1_WT.pdb, etc. Generate point mutants (A1708E, M1775R on BRCA1; R2336H, D2723H on BRCA2): In Discovery Studio “Mutagenesis” tool → choose rotamer library Energy‐minimize side chains (Steepest‐Descent, 2000 steps) Export each as e.g. BRCA1_A1708E.pdb 2. Run HDOCK Docking For each receptor–ligand pair (WT & mutant × hK1–hK4): Navigate to http://hdock.phys.hust.edu.cn/ Select “Protein–Protein Docking” Upload files Receptor: Receptor_minimized_structures/BRCAx_*.pdb Ligand: corresponding kallikrein PDB Chain IDs: keep original chain labels (e.g. A for BRCA, B for kallikrein) Mode: Template-free docking (default) Scoring: Default HDOCK scoring function (hybrid physics + statistics) Submit job and wait (~5–10 min per job) Download the top 10 ranked models into Docking/BRCAx-hKy/model_1.pdb through model_10.pdb 3. Interface Analysis with PDBePISA For each top-ranked model: Go to https://www.ebi.ac.uk/pdbe/pisa/ Upload the PDB (model_1.pdb) Run “Assembly and Interface” analysis Download reports: Interface summary XML/PDF → save in Docking_interactions/BRCAx-hKy/Chains.pdf Detailed contacts list → save as interactions.pdf Export interface metrics (buried area, ΔG solvation) into interface_stats.xlsx 4. Compile and Visualize Results Open binding_energies.xlsx to view HDOCK docking scores for all 16 complexes. Load interface_stats.xlsx into Excel or R/Python to correlate solvation ΔG vs. docking score. Inspect key residue contacts in key_interactions.docx alongside the interactions.pdf outputs. Visualize representative complexes in PyMOL or Chimera using the PDBs under Docking/…/model_1.pdb.