Protein Inception
October 09, 2023Protein design by hallucination. DeepDream, Markov Chain Monte Carlo (MCMC), KL divergence, gradient optimization, scaffolding functional sites, SARS-CoV-2 receptor traps.
Written by Liam Bai who lives and works in Boston trying to build useful things. He's on LinkedIn and Twitter.
How to represent a protein sequence
September 29, 2023Learning protein representations. Transfer learning, protein language models, contextual embeddings, Transformers, masked language modeling, BERT, UniRep, ESM, attention analysis.
What we can learn from evolving proteins
September 12, 2023Predicting protein structure and function. Multiple Sequence Alignments (MSAs), the protein folding problem, the Potts model, Direct Coupling Analysis (DCA), EVCouplings.