[MD-4] Script based Docking & Analysis using Discovery Studio & PLIP

Please do remember to cite this paper for the methodology used.
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" Firoz A, Talwar P. Role of death-associated protein kinase 1 (DAPK1) in retinal degenerative diseases: an in-silico approach towards therapeutic intervention. J Biomol Struct Dyn. 2024 Jul;42(11):5686-5698. doi: 10.1080/07391102.2023.2227720. Epub 2023 Jun 30. PMID: 37387600."
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This video demonstrates the Molecular Docking with Autodock Vina using the Perl script. Perl is already installed in the latest version of ubuntu. The Video also summarize how to perform swissadme for the pubchem compounds for analysing the druglikeness and finally the analysis of protein ligand complex using BioVia DIscovery Studio and PLIP (Protein-Ligand Interaction Profiler)

Save the below mentioned files in the main directory where you are going to execute docking.

1. Perl Script - https://drive.google.com/file/d/1AS3I...
2. Configuration file - https://docs.google.com/document/d/1Y...

Edit the configuration file based on your receptor name, coordinates and Dimension Keep the mode and exhaustive number as default.

Molecular Docking Tutorial Playlist
1. How to Install Linux SubSystem in Windows for Molecular Docking -    • [MD-1] How to Install Linux SubSystem in W...  
2. Protein Preparation for Molecular Docking -    • [MD-2] Protein Preparation for Molecular D...  
3. Ligand Screening and Preparation for Molecular Docking -    • [MD-3] How to download 100s of Ligands & P...  
4. Script based Molecular Docking and Analysis -    • [MD-4] Script based Docking & Analysis usi...  

Online Tools
1. Swiss ADME - http://www.swissadme.ch/ | Click to watch at 03:17
2. PubChem ID Exchanger - https://pubchem.ncbi.nlm.nih.gov/idex... | Click to watch at 03:54
3. PLIP - https://plip-tool.biotec.tu-dresden.d... | Click to watch at 07:10

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