Computational Data for Anti-inflammatory Effects of Water-Soluble Polysaccharides from Annona squamosa L. Fruit Pulp (WPAS): DFT, Network Pharmacology, Molecular Docking, and MD Simulations

Description

This dataset includes raw and processed files from DFT descriptor profiling, network pharmacology analysis, molecular docking results (PDBQT, docking poses, binding energies), and molecular dynamics simulations (trajectories, RMSD/RMSF plots, input topologies, output files from AMBER or similar software) for interactions between WPAS monosaccharide motifs and MMP9 targets.

Steps to reproduce

To reproduce the computational results in this dataset: 1. DFT descriptor profiling: Use Pis4 or similar software with B3LYP/6-31G level to calculate descriptors for WPAS monosaccharide motifs . Input structures from PubChem or optimized geometries. 2. Network pharmacology: - Predict targets using SwissTargetPrediction or PASS for monosaccharide motifs. - Retrieve disease targets from GeneCards/DisGeNET. - Identify intersections via Venny or jvenn tool. - Construct PPI network with STRING; perform GO/KEGG enrichment with DAVID or clusterProfiler. 3. Molecular docking: - Prepare receptor (MMP9 PDB ) using AutoDock Tools (remove water, add hydrogens). - Ligands: monosaccharide structures in PDBQT format. - Run docking with AutoDock Vina or AutoDock4; analyze poses and binding energies in PyMOL or Discovery Studio. 4. Molecular dynamics simulations: - Use GROMACS (or AMBER): Generate topology with ACPYPE or tleap for ligands/protein. - Solvate in TIP3P water box, add ions, minimize, equilibrate (NVT/NPT), produce 100 ns production run. - Analyze trajectories: gmx rms/rmsf for RMSD/RMSF; gmx energy for potential energy; visualize in VMD. Software versions and parameters are detailed in the README.txt file within the dataset folders. All scripts (.sh, .py) for automation are included in /Scripts folder. For exact commands, refer to the input files (.mdp, .top) and log files.

Institutions

• Guangdong Pharmaceutical University

  Guangdong, Guangzhou

Categories

Funders

• This research was supported by the Zhongshan Tiantu Fine Chemical Co., Ltd.–Guangdong Pharmaceutical University Joint R&D Fund.

  Grant ID: No. TTGY202508

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