Screening and Mechanistic Analysis of Hypoxia-Tolerant Bioactive Components from traditional Chinese medicines Based on Network Pharmacology , Molecular Docking and Molecular Dynamics Simulation
Description
Initial Data and Processing Results for the Screening and Mechanistic Analysis of Hypoxia-Tolerant Bioactive Components from Traditional Chinese Medicines Based on Network Pharmacology, Molecular Docking, and Molecular Dynamics Simulation
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Steps to reproduce
1. Identify active components of traditional Chinese medicine from the Herb, SymMap (http://www.symmap.org/), TCMID (http://www.megabionet.org/tcmid/), and TCMSP (https://www.tcmsp-e.com/load_intro.php) databases. 2. Predict component targets using Swiss TargetPrediction. 3. Obtain hypoxia-related targets from the PharmGKB (https://www.pharmgkb.org/), OMIM (https://omim.org), Genecards (https://www.genecards.org), and Disgenet (https://disgenet.com/) databases. 4. Constructed protein-protein interaction (PPI) networks using the String database (https://cn.string-db.org/) and visualized them with Cytoscape. 5. Performed Gene Ontology (GO) analysis using the DAVID database (https://david.ncifcrf.gov) and KEGG analysis using the KOBAS database (https://bioinfo.org/kobas). 6. Generated a large network diagram using Cytoscape 3.8.0. 7. Performed molecular docking using Autodock and PyMOL. 8. Conducted molecular dynamics simulations with GROMACS.