Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
Application: An AI Agent for Protein and Molecular Design I’m developing an AI agent for protein and molecular design - an autonomous system that can take a high-level design brief (e.g. “design a protein that binds target X with nanomolar affinity”) and execute the full computational design pipeline: searching structure databases, running generative models, evaluating candidates, iterating on designs, and preparing sequences for synthesis. Unlike standalone models, an agent orchestrates multiple tools and makes decisions across the design cycle with minimal human intervention.
Week 2 HW: DNA Read, Write, and Edit
Part 1: Benchling Gel Art Virtual restriction digest of Lambda DNA (J02459) using EcoRI, HindIII, BamHI, PstI, SalI, and XhoI, visualized in NEBcutter. Part 3: DNA Design Challenge 3.1 Choose Your Protein I chose endoglucanase A (CelCCA) from the bacterium Clostridium cellulolyticum. This organism has since been reclassified as Ruminiclostridium cellulolyticum. The crystal structure of its catalytic domain is in the PDB as entry 1EDG. It was solved at 1.6 angstrom resolution.
Part 1: Opentrons Art I designed my artwork using the Automation Art GUI at opentrons-art.rcdonovan.com. I uploaded a bat image and the tool pixelated it into dispensing coordinates for three fluorescent proteins: mClover3 (green, 41 points), mRFP1 (red, 393 points), and Azurite (blue, 40 points). The design uses 0.75 µL droplet sizes at 2.2 mm spacing.