Protein ML Talks
Recent talks applying the latest protein-ML models for design under the framework of p(sequence, structure, function).
»Protein ML Colab Notebooks
Seven Google Colab notebooks made for the CSBERG Synthetic Biology course. Content delivered in Summer 2021.
»NeuralODE for Gene Network Design
Colab notebook for designing gene regulatory networks by specifying desired dynamics then backproping through an ODE solver.
»Potts Model Visualized
Inspired by The Illustrated Transformer, this post unpacks the symbols behind a Potts Model and visualizes how its parameters help us understand the evolution of protein sequence and structure.
»Generative Enzymes Model
Adapting the CbAS algorithm to generate plastic degrading enzymes with information from structure.
»Protein Structure Design
Lab meeting slides at Philip Kim’s group on classical and machine learning guided protein design, with a walkthrough of how to use MaSIF to search for DNA mimicking proteins in the PDB.
»Protein Design Lectures
The lectures on protein design below are part of a summer workshop series on synthetic biology organized by he Canadian Synthetic Biology Education Research Group CSBERG.
»Optimizing Plastic Degrading Proteins
We present a generalizable and automated pipeline for protein design. Our model can be applied to the optimization of any protein class, even those with scarce data.
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