Ligand Optimization required or not for Molecular Docking
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The presentation discusses the necessity of ligand optimization and minimization in molecular docking, highlighting various factors and challenges such as cleaning, optimization processes, and false positives. It mentions that crystal structures from the CSD database may not require optimization unless specific needs arise. The importance of starting with good structures and utilizing conformer variations is emphasized.
Ligand Optimization required or not for Molecular Docking
- 1. Ligand Optimization/ Minimization required or not for Molecular Docking? Girinath G Pillai, PhD @giribio
- 2. ● Slides contains contents/pictures/videos taken from web, articles, lectures, tutorials and its respective authors own their copyrights. Technical Slides : slideshare.net/giribio Case Studies : youtube.com/giribio Workflows & Notebooks : github.com/giribio
- 3. The Concerns! Cleaning ● Non ionized ● Counter ions ● Chemical reactive moiety ● Promiscuous binders ● Fluorescent molecules (dyes) ● Redundancy ● Diversity ● De-Salt process ● Racemates?? Optimization ● Bond length ● Bond angle ● Dihedrals ● Stereochemistry ● Steric hindrances ● Charges/Valency Minimization Steepest Descent FFs - MMFF94, UFF, etc False positives/artificats
- 4. Challenges deep-dive Crystal Structures Minimize or not? CSD database structures need not to be minimized. If some specific requirement a single point calculation could help. 2D Structures Drawn or Downloaded Explicit Hydrogens were added Ensure 2D to 3D optimization is taken care. Conformers Ring and others Boat and Chair conformers delivers different activity Good starting structures are required
- 7. Thanks! @giribio LLB members, Dhivya, Thirumal, Jitesh Next topic: 3D QSAR?
- 8. Solution More premium subscribers Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.