Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
- First, describe a biological engineering application or tool you want to develop and why. I am interested in developing materials that recover over time by mimicking fungal evolutionary conservatism and continuity. I am currently developing a pollen sensor intended to be placed in children’s playgrounds, while simultaneously reading Merlin Sheldrake’s Entangled Life. Together, these are inspiring me to think about design in a different way.
Week 2 HW: DNA Read, Write, Edit Life
Part 1: Benchling & In-silico Gel Art Navigating to Lambda sequence and saving as text. file Importing Lambda file by saving FASTA Format of Sequence file Simulate Restriction Enzyme Digestion with the following Enzymes: EcoRI Testing Virtual digest example Adding more restrcition enzymes Simulate Restriction Enzyme Digestion with all the Enzymes
Generate an artistic design using the GUI at opentrons-art.rcdonovan.com I wanted to draw Punch, the famous baby Japanese macaque from the zoo in Japan. The GUI created an approximate outline which I used as a base and added more details of different colour on top. This was the end result This was the settings with the coordinates.
Week 4 HW: Protein Design Part I
Part A. Conceptual Questions Answer any NINE of the following questions from Shuguang Zhang: (i.e. you can select two to skip) How many molecules of amino acids do you take with a piece of 500 grams of meat? (on average an amino acid is ~100 Daltons) meat is around 20-27 percent for beef. 500 x 0.20 =100 grams of protein 1 Dalton = 1.66054e-24 grams 1 amino acid = 110 Daltons
Week 5 HW: Protein Design Part II
Part A: SOD1 Binder Peptide Design (From Pranam) Your challenge: Design short peptides that bind mutant SOD1. Then decide which ones are worth advancing toward therapy. You will use three models developed in our lab: PepMLM: target sequence-conditioned peptide generation via masked language modeling PeptiVerse: therapeutic property prediction moPPIt: motif-specific multi-objective peptide design using Multi-Objective Guided Discrete Flow Matching (MOG-DFM) Part 1: Generate Binders with PepMLM Begin by retrieving the human SOD1 sequence from UniProt (P00441) and introducing the A4V mutation. Using the PepMLM Colab linked from the HuggingFace PepMLM-650M model card: Generate four peptides of length 12 amino acids conditioned on the mutant SOD1 sequence. To your generated list, add the known SOD1-binding peptide FLYRWLPSRRGG for comparison. Record the perplexity scores that indicate PepMLM’s confidence in the binders. Part 2: Evaluate Binders with AlphaFold3