Data for Identifying therapeutic potential of Dioscorea alata for treating Alzheimer's Disease
Description
This dataset was collected, cleaned and curated for our research project to find therapeutic potential of Dioscorea alata (Purple yam) for Alzheimer's Disease. The data includes compounds present in Dioscorea alata, the genes involved in Alzheimer's and intersection of genes that interacted with compounds. These interactions were observed and visualized, to understand how these compounds are related with the Alzheimer's Disease markers and had significantly for their role in neuroprotection and anti-inflammatory pathways.
Files
Steps to reproduce
Softwares/Programming Language Used: 1. MS Excel (Storing and Cleaning data) 2. Python (Automating SMILES retrieval from PubChem REST API and automating multiple ligand docking) 3. CytoScape (For Network Analysis and Visualization) 4. Autovina and Biovia Discovery Studio (For Molecular Docking and Visualization) Databases/Web-based tools: 1. CTD, DisGeNET and GeneCards (Alzheimer's Disease Markers) 2. IMPPAT, KNApSAcK and Dr. Duke's Database (Compounds of Dioscorea alata) 3. SwissADME and TargetNET (for evaluating Druglikeness and Bioavailability (using Lipinski's Rule)) 3. SEA Database and SuperPred (Target Prediction and Compound-Gene Interactions) 4. Pathlinker and CytoHubba (plugins in CytoScape for sorting top 20 networks based on degree and closeness) 4. STRING-DB (for Protein-Protein Interaction (PPI) Network) 5. ShinyGO (For Gene Ontology and Enrichment Analysis and KEGG Pathway) For any other queries: Please reach out to corresponding author.
Institutions
- University of Mumbai
- Bombay College of Pharmacy