Nathan welcomes back computational biochemist Amelie Schreiber for a fascinating update on AI's revolutionary impact in biology. In this episode of The Cognitive Revolution, we explore recent breakthroughs including AlphaFold3, ESM3, and new diffusion models transforming protein engineering and drug discovery. Join us for an insightful discussion about how AI is reshaping our understanding of molecular biology and making complex protein engineering tasks more accessible than ever before.

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CHAPTERS:

(00:00:00) Teaser

(00:00:46) About the Episode

(00:04:30) AI for Biology

(00:07:14) David Baker's Impact

(00:11:49) AlphaFold 3 & ESM3

(00:16:40) Protein Interaction Prediction (Part 1)

(00:16:44) Sponsors: Shopify | SelectQuote

(00:19:18) Protein Interaction Prediction (Part 2)

(00:31:12) MSAs & Embeddings (Part 1)

(00:32:32) Sponsors: Oracle Cloud Infrastructure (OCI) | Weights & Biases RAG++

(00:34:49) MSAs & Embeddings (Part 2)

(00:35:57) Beyond Structure Prediction

(00:51:13) Dynamics vs. Statics

(00:57:24) In-Painting & Use Cases

(00:59:48) Workflow & Platforms

(01:06:45) Design Process & Success Rates

(01:13:23) Ambition & Task Definition

(01:19:25) New Models: PepFlow & GeoAB

(01:28:23) Flow Matching vs. Diffusion

(01:30:42) ESM3 & Multimodality

(01:37:10) Summary & Future Directions

(01:45:34) Outro

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