Docking dataset: Caffeic acid with TAK1, AMPK, and TJ-related proteins

This dataset provides all molecular docking input and output files for caffeic acid docked to TAK1, AMPK, and tight junction–related proteins (ZO-2, Claudin-1, Claudin-3, and Claudin-4) using AutoDock Vina (v1.1.2; exhaustiveness = 32; three independent runs per target). The dataset includes prepared receptors and ligands, configuration files, log files, selected best-scoring poses, complex structures, and docking results for property-matched decoy molecules to support independent verification and reproducibility.

<Data Description for Molecular Docking Analysis>

This repository contains the complete dataset for molecular docking simulations between Caffeic acid and its target proteins (TAK1, AMPK, ZO-2, Claudin-1, -3, -4). This description provides a detailed roadmap of the uploaded files to facilitate peer review during the embargo period.

1. Repository Organization
The data are structured into six primary directories, one for each target protein: /TAK1/, /AMPK/, /ZO2/, /Claudin1/, /Claudin3/, /Claudin4/

Each directory contains all necessary files to replicate the docking process and verify the results presented in the manuscript.

2. Detailed File Descriptions (per Target Directory)
To ensure transparency, each folder contains the following standardized file sets:

Receptor Preparation: 
- *_original.pdb: The initial protein structure.
- *_prepared.pdb & *.pdbqt: The final receptor structures used for docking after removing water molecules and assigning charges.

Docking Execution:
- *_config.txt: The AutoDock Vina configuration file. This includes the exact grid box center coordinates, dimensions, and exhaustiveness (32), allowing reviewers to verify 
  the search space. 

Results & Reproducibility:
- *_out(Figure).pdbqt: The specific docking pose that corresponds to the visualization in the manuscript (e.g., Figure 8).
- *_out2.pdbqt & *_out3.pdbqt: Results from independent docking runs to demonstrate the consistency of the binding mode.
- *_log(Figure).txt, *_log2.txt, *_log3.txt: Raw log files showing the predicted binding affinities (kcal/mol) for each run.

Complex Structure:
- *_complex.pdb: A pre-assembled protein–ligand complex file for immediate structural assessment.

3. Decoy-Based Validation Data
The /decoys/ subdirectory contains the following files to support the specificity of Caffeic acid:

*_decoy_Results.csv (or .xlsx): A compilation of docking scores for property-matched decoy molecules. These data provide a statistical baseline used to assess whether the 
docking score of caffeic acid is distinguishable from property-matched non-active analogs.

4. Correspondence with Manuscript
Table Data: All binding energy values reported in the manuscript tables correspond to the lowest-energy pose from the docking run designated for figure visualization 
(*_log(Figure).txt).

Visual Figures: The 3D interactions and 2D ligand–protein interaction maps (e.g., LigPlot+) shown in the figures were generated based on the *_out(Figure).pdbqt files.