Learnt major carbapenemase genes (KPC, NDM, OXA) using NCBI isolate data and molecular dynamics. Includes gene frequency trends, co-resistance patterns, and MM/PBSA binding comparisons of avibactam with KPC vs NDM to illustrate mechanistic differences 🧬
🧬 Testing beta-lactamase resistance with AlphaFold + DiffDock + GROMACS! Watch clavulanic acid bind TEM-5, CTX-M-15, KPC-2, and get rejected by TEM-30. Simulation confirms biology! 🔬💊
🧬 Explored molecular docking & MD simulations with penicillin binding to PBP2x — lots of stumbling through GROMACS but slowly piecing it together! 💊 Still much more to learn, but we’re getting there! 🔬
Enjoyed learning the process of setting up a cluster of tiny PCs for parallel computing. A note to myself on installing Ubuntu, passwordless SSH, automating package installation across nodes, distributing R simulations, and comparing CV5 vs CV10 performance. Fun project!
Testing Super Learner with TMLE showed some interesting patterns 🤔 XGBoost + random forest only hit ~54% coverage, but tuned xgboost + GLM reached ~90%. Seems like pairing flexible learners with stable (even misspecified) models helps? Need to explore this more with different setups 📊