Computer Aided Drug Designing (Practical Session) скачать в хорошем качестве

Computer Aided Drug Designing (Practical Session)

This is a recorded version of class that was conducted during the lockdown period due to Covid-19 pandemic. In this video, practical demonstrations have been given on how to find a drug target from literature and how to get its structure from PDB Database, how the complexed ligand (if any) is removed. On the other hand, I have shown how to retrieve ligand structures from PubChem Compound or ChEMBL database. Free online tools like MolSoft Drug Likeness tool was used to draw and predict Lipinski and Drug Likeness properties. Online CORINA Demo was used to generate PDB structure of the ligand from SMILES format. Again we have discussed the ADMET Screening using Mobyle@RPBS as well as pkCSM online servers. The molecular docking experiment has been performed in AutoDock Vina using the Python Molecule Viewer GUI. The interpretation of the results have also been discussed and the interactions are visualized in LigPlot+ software. To do the practical, you will need to install the following softwares: 1) AutoDock Vina: http://vina.scripps.edu/download/auto... 2) MGL Tools (PMV): http://mgltools.scripps.edu/downloads... 3) For analysis, LigPlot+ is a good software. But for that you will need an academic email. If you have an academic email id, you may download it from here after registration: https://www.ebi.ac.uk/thornton-srv/so... or you may download PyMol and UCSF Chimera to do the Hydrogen Bond analysis: PyMol: https://pymol.org/installers/PyMOL-2.... Chimera: https://www.cgl.ucsf.edu/chimera/cgi-... And you must have RasMol as well: http://www.rasmol.org/software/RasMol... So, these softwares are sufficient for the practicals. But, you will need the files which are used in this video. a) For the Target Protein Structure, download this: https://files.rcsb.org/download/5UPJ.pdb (The downloaded file has been renamed as "HIV2P.pdb" in the video). b) For the ligand (Nelfinavir) structure, copy the following SMILES String: CC1=C(C=CC=C1O)C(=O)NC(CSC2=CC=CC=C2)C(CN3CC4CCCCC4CC3C(=O)NC(C)(C)C)O and convert it to 3D structure in PDB Format using the CORINA server (https://www.mn-am.com/online_demos/co.... Detailed steps are given in the video. I hope this video will help you in doing the practical on Basics of Computer Aided Drug Designing. Thank you.