https://pages.htgaa.org/2026b/casian-veselin/homework/index.htmlWeekly homework submissions: Week 1 HW: project ideasHugoenhttps://pages.htgaa.org/2026b/casian-veselin/homework/week-01-hw-project-ideas/index.htmlMon, 01 Jan 0001 00:00:00 +0000https://pages.htgaa.org/2026b/casian-veselin/homework/week-01-hw-project-ideas/index.htmlWhat do you want to make? → Custom designed protein; post translational modifications/ usage of nonstandard amino acids (e.g. selenocysteine) not clear. For the purpose of this homework, may the custom protein be named Cuop. Coup is a peptidic macromolecule I plan to design, analyse and test using various computational tools. Its intended goal is to address prion activity in-vivo; work like an inhibitory drug against prion PrPSc “infectious” folding mechanism. The explanation for a protein’s ability to self-propagate a motif is intermolecular interactions between strongly bound-together amino acids (PrPSc beta sheets) and a less rigid structure (PrP alpha helices). Therefore a molecule able to prevent the interactions between the two proteins may be capable of preventing the spread of disease in high risk patients. The way I aim to achieve this is molecular docking simulations to assess if the custom protein can actually help.https://pages.htgaa.org/2026b/casian-veselin/homework/week-02-hw-kernel/index.htmlMon, 01 Jan 0001 00:00:00 +0000https://pages.htgaa.org/2026b/casian-veselin/homework/week-02-hw-kernel/index.htmlProtein expression system in Asimov Kernel 1. Defining expression target What molecule are you expressing? A protein, an RNA, or an enzyme (or small set of enzymes) for a pathway. If your HW1 product is a material, food, or chemical, identify the protein(s) that produce it and design for those. Fortunately, the only molecule desribed for my final project is a single short protein (i.e. prion-binding ‘peptide’). The design logic stays simple throughout production: DNA -> mRNA -> protein of interest.https://pages.htgaa.org/2026b/casian-veselin/homework/week-03-cfps/index.htmlMon, 01 Jan 0001 00:00:00 +0000https://pages.htgaa.org/2026b/casian-veselin/homework/week-03-cfps/index.htmlWEEK 3 ASSIGNMENT: CFPS REACTION DESIGN FOR SFGFP, PETASE, RETEPLASE A. COMPARE CELL-FREE REACTION COMPOSITIONS (20 minutes) Why does the concentration of potassium glutamate and magnesium glutamate differ between compositions? Which is more sensitive? Referance concentration: K-glutamate (279.84 mM), Mg-glutamate (8.22 mM) are to mimic and maintain osmotic parameters of lysate in CFPS, assure ribosome, energy-replenishing enzymes, polymerase function, stabilise DNA/RNA structure etc.; both glutamic acid salts are usually found in high concentrations.https://pages.htgaa.org/2026b/casian-veselin/homework/week-04-cfps/index.htmlMon, 01 Jan 0001 00:00:00 +0000https://pages.htgaa.org/2026b/casian-veselin/homework/week-04-cfps/index.html