Sample interview questions: Can you discuss your experience in using molecular docking techniques?
Sample answer:
- Experience with a variety of molecular docking software:
- Successfully employed programs such as AutoDock, AutoDock Vina, and Glide for virtual screening and lead optimization projects.
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Proficient in using software features like flexible docking, induced fit docking, and molecular dynamics simulations.
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Expertise in preparing protein and ligand structures for docking:
- Generated high-quality protein structures through homology modeling, crystal structure refinement, and molecular dynamics simulations.
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Performed ligand preparation tasks, including energy minimization, protonation state assignment, and removal of unwanted atoms.
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Strong understanding of molecular docking theory and scoring functions:
- Comprehend the principles underlying different scoring functions, including empirical, force field-based, and knowledge-based approaches.
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Evaluated the accuracy and reliability of scoring functions through benchmark studies and validation experiments.
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Ability to analyze and interpret docking results:
- Analyzed docking poses for binding mode predictions, hydrogen bonding interactions, and hydrophobic contacts.
- Identified key interactions responsible for ligand binding and selectivity.
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Generated contour maps and heat maps to visualize the distribution of binding energies and interactions.
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