---
date: 2024-11-21
type: daily
tags: [lab-notes]
---

# 2024-11-21 - Thursday

## Experiments

CRISPR screen transduction day.

- Transduced HCC827 and MDA-MB-231 with pooled library
- MOI 0.3 (low, minimize doublets)
- 10M cells per line transduced
- Selection starts Saturday (puromycin 2 μg/mL)

## Analysis

Prepared for tomorrow's docking:
- Retrieved [[AlphaFold]] EGFR structure from [[Experiment-2024-10-28]]
- [[Validated]] against PDB 1M17 (RMSD 0.8 Å) ✓
- Prepared with Schrödinger wizard
- [[Defined]] ATP binding [[Site]] (15 Å box)

Downloaded [[Top 10]] compounds from [[Experiment-2024-11-20]]:
- Converted SMILES to 3D ([[OpenBabel]])
- Energy minimized (MMFF94)
- [[Ready]] for [[AutoDock]] Vina

## Computation

Set up MD simulations for [[Top]] 3 docking hits:
- [[AMBER Force Field]] (ff19SB + GAFF2)
- 100 ns [[Production]] [[Each]]
- GPU cluster reserved for weekend

## [[Papers Read]]

[[Karplus2002-Molecular-Dynamics]] - [[Nobel Prize]] work, [[Excellent]] review.

## [[Next Steps]]

- Molecular docking ([[Friday]])
- [[Launch]] MD simulations (Friday evening)
- CRISPR selection starts Saturday

## [[Notes]]

AlphaFold structures [[Are]] docking-ready. [[Computational]] drug discovery is [[Now]] feasible without crystal structures.
