Molecular docking data for β-1,3-glucan ligands with Dectin-1, MMP-2 and MMP-9
Description
This dataset contains the molecular docking data generated for the study entitled “Alum-assisted silk fibroin/paramylon-coated cellulose sponge as a β-glucan-releasing ECM-mimetic biomaterial for chronic wound healing.” Molecular docking was performed to explore the possible interactions of representative β-1,3-glucan ligands—glucose, laminaritriose and a β-1,3-glucan hexamer—with Dectin-1, matrix metalloproteinase-2 (MMP-2) and matrix metalloproteinase-9 (MMP-9). The dataset includes ligand and receptor PDB structures, docked poses, binding-affinity and RMSD results, and representative 2D and 3D interaction images. Blind docking was performed using AutoDock Vina through PyRx with the search space covering the entire receptor structure. The best-ranked pose was selected based on the lowest binding-affinity score. The data are provided to support transparency and reproducibility of the computational analysis. Docking results should be interpreted as exploratory evidence of possible ligand–target interactions and not as direct evidence of Dectin-1 activation or MMP inhibition.
Files
Steps to reproduce
Molecular docking was performed using AutoDock Vina through PyRx. The protein targets Dectin-1, MMP-2 and MMP-9 were prepared by removing water molecules and unnecessary heteroatoms, followed by addition of polar hydrogens and charge assignment. Glucose, laminaritriose and β-1,3-glucan hexamer were used as ligands and were energy-minimized before docking. Blind docking was performed using a search space covering the entire receptor structure. For each ligand–target combination, the best-ranked pose was selected based on the lowest binding-affinity score. Docking poses and molecular interactions were visualized using BIOVIA Discovery Studio Visualizer 2021. The corresponding PDB files, docking output CSV files and interaction images are provided in this dataset.
Institutions
- Anna University, ChennaiTamil Nadu, Chennai