The Future of AI Molecular Discovery

During last month’s NeurIPS 2025 conference, YC’s Ankit Gupta sat down with Ellen Zhong, an assistant professor of computer science at Princeton, to discuss how machine learning is reshaping structural biology. They explore how proteins aren’t static structures but dynamic molecular machines, and how techniques like cryo-electron microscopy combined with ML are revealing protein motion beyond traditional structure prediction. The conversation also dives into inverse problems, noisy experimental data, and what’s next for AI-driven scientific discovery. Chapters 00:11 — Introduction 00:55 — From Supercomputers to Cryo-EM 02:43 — The Rise of Cryo-EM 03:30 — Proteins as Dynamic Systems 04:30 — Inverse Problems in Biology 05:31 — Lessons from DeepMind, Industry and Academia 07:35 — Why Protein Dynamics Remain Unsolved 08:29 — Collaborating with Experimental Scientists 09:28 — What’s Overhyped and Underhyped in AI-Driven Biology 10:51 — The Future of AI-Driven Biology Apply to Y Combinator: https://www.ycombinator.com/apply Work at a startup: https://www.ycombinator.com/jobs

Ankit GuptahostEllen Zhongguest

Jan 24, 202611mWatch on YouTube ↗

EPISODE INFO

Released: January 24, 2026
Duration: 11m
Channel: YC Root Access
Watch on YouTube: ▶ Open ↗

EPISODE DESCRIPTION

During last month’s NeurIPS 2025 conference, YC’s Ankit Gupta sat down with Ellen Zhong, an assistant professor of computer science at Princeton, to discuss how machine learning is reshaping structural biology. They explore how proteins aren’t static structures but dynamic molecular machines, and how techniques like cryo-electron microscopy combined with ML are revealing protein motion beyond traditional structure prediction. The conversation also dives into inverse problems, noisy experimental data, and what’s next for AI-driven scientific discovery. Chapters 00:11 — Introduction 00:55 — From Supercomputers to Cryo-EM 02:43 — The Rise of Cryo-EM 03:30 — Proteins as Dynamic Systems 04:30 — Inverse Problems in Biology 05:31 — Lessons from DeepMind, Industry and Academia 07:35 — Why Protein Dynamics Remain Unsolved 08:29 — Collaborating with Experimental Scientists 09:28 — What’s Overhyped and Underhyped in AI-Driven Biology 10:51 — The Future of AI-Driven Biology Apply to Y Combinator: https://www.ycombinator.com/apply Work at a startup: https://www.ycombinator.com/jobs

SPEAKERS

Ankit Gupta
host
YC interviewer/host for the episode.
Ellen Zhong
guest
Assistant professor at Princeton focusing on machine learning for molecular discovery and structural biology (e.g., cryo-EM, protein dynamics).

EPISODE SUMMARY

In this episode of YC Root Access, featuring Ankit Gupta and Ellen Zhong, The Future of AI Molecular Discovery explores aI meets cryo-EM to reveal protein motions and discovery Zhong’s lab applies machine learning to inverse problems in structural biology, especially reconstructing protein structures and dynamics from noisy cryo-EM images.

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