Cloud-based Hands-on Workshop:

Computational Structure-based Screening and Explicit Molecular Dynamics

ug

and

r

Two-day cloud-based hands-on workshop targeting structure-based drug designing and MD simulations. Participants will get practical experience and in-person guidance on the Maestro GUI, organic molecule sketching, protein selection preparation, and screening for hit identification of molecules against therapeutic targets. The workshop will also include a brief recap of background theory for Molecular mechanics, CADD, Structure-based drug design approaches via case studies on the real-time industrial projects.

Time 09.30 10.00 10.10 10.30 11.00 11.20 11.35 11.45 12.10 12.30 13.00 14.00 14.25 14.40 14.55 15.30

15.55 16.30

Session Technical setup - Audio & Visual check Agenda and breakout rooms exercise Breakout - Introductions and launching software Presentation- Maestro GUI: Building Molecules and Enumeration Breakout - Build Chalcones from SMILES Presentation - Ligand Preparation and ADME Breakout - Launch LigPrep Presentation - Molecular Docking, Protein and Ligand Preparation Presentation - Protein Preparation and Grid Generations Breakout - Protein prep, grid generation and molecular docking Lunch Break Presentation - Molecular Docking Breakout - Analyzing 3D molecular docking analysis Presentation - Molecular Docking Analysis Breakout - 2D molecular docking analysis Revision of Day 1 Breakout - Practice Wrap-up and Q/A Finish

--------------------------------------------------------------------------------------------------------

-------------------------------------------------------------------------------------------------------- Day 1 Schedule

Date: 05 - 06 October, 2021thth th

Day 2 Schedule Time Session 9.30 Technical set-up and Audio & Visual check 10.00 Presentation- Molecular dynamics theory 10.30 Breakout - Docking results and ligand sketching 10.45 Presentation - Desmond Introduction 11.00 Breakout - Protein ligand complex formation, system building 11.15 Presentation - Molecular Dynamics Demo 11.25 Breakout - MD submission 11.35 Presentation - Desmond Trajectory Visualization 11.50 Breakout - Participant analysis 12.15 Lunch Break 14.00 Presentation - Desmond Molecular Simulation Analysis 14.20 Breakout - Analyzing 3D molecular docking analysis 14.45 Presentation - Organic Molecules Enumeration 15.00 Breakout - Reaction-based enumeration, library enumeration, ADME 15.30 Full Revision of Day 2 15.55 Wrap-up and Q/A 16.30 Finish

Coordinators: Dr. Vengadesan KrishnanDr. Deepti JainDr. Prem S KaushalProf. Deepak T Nair

Registration: Registration is open to limited participants.

Registration link here: t.ly/gyT6

Last date of registration: Sept 25th 2021

Hardware Requirement: Computer/Laptop, Chrome browser, Internet

connection (~8Mbps)