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Intro to Deep Learning for Protein Design
This video introduces the fundamentals of protein design and summarizes the trajectory of the course with a focus on (1) the foundational biochemistry that protein structure prediction and design hinge on and (2) deep learning / machine learning principles overview.
Video from the Rosetta Commons PPI Workshop (February 2025)
Video Instructor: Amrita Nallathambi (UNC Chapel Hill)
Credits:
Instructor: Amrita Nallathambi
Teaching Assistants: Yehlin Cho, Cyrus Haas, and Matthew Hvasta,
RC Leadership and NSF Sponsor Grant PIs: Julia Koehler Leman & Jeffrey Gray
RC Education Director: Ashley Vater
Videographer: Canyon Florey
Rosetta Workshop Participants
00:00 - Introduction
00:20 - Deep Learning Revolution for Proteins
01:50 - The Transformer
03:38 - AlphaFold2 Overview
06:22 - AlphaFold2 Inputs
09:48 - AlphaFold2 Outputs
13:29 - Graph Neural Networks
16:24 - ProteinMPNN Loss
17:35 - Diffusion models
18:30 - RFDiffusion
19:52 - Inputs and Outputs
20:43 - Potentials
