Machine Learning Applied to Macromolecular Structure and Function (X5)
March 23-26, 2025
| Keystone Resort, Keystone, CO, United States
Mohammed AlQuraishi, Elizabeth Kellogg and Possu Huang
Scholarship Deadline: Jan. 24, 2025 | Abstract Deadline: Feb. 28, 2025 | Early Registration Deadline: Feb. 5, 2025
| 4:00–8:00 PM |
Registration |
Longs Peak Foyer |
| 6:00–8:00 PM |
Welcome Mixer |
Longs Peak Foyer |
| 7:00–8:00 AM |
Breakfast |
Shavano/Torreys Peaks |
| 8:00–9:00 AM |
Welcome and Keynote Address (Joint) |
Longs Peak / Grays Peak |
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* Elizabeth Villa, University of California, San Diego
Session Chair |
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* Mohammed AlQuraishi, Columbia University
Session Chair |
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Wolfgang P. Baumeister, Max Planck Institute of Biochemistry
Cryo-Electron Tomography or the Power of Seeing the Whole Picture |
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| 9:00–11:30 AM |
Machine Learning for Protein Structure (Joint) |
Longs Peak / Grays Peak |
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* Julia Rogers, Columbia University
Session Chair |
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Hannah Wayment-Steele, University of Wisconsin-Madison
Have Protein Language Models Learned Dynamics |
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Sergey Ovchinnikov, MIT
Hacking AlphaFold to Do New Things |
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* Mohammed AlQuraishi, Columbia University
Understanding How AlphaFold Learns |
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Fabian C Spoendlin, University of Oxford
Short Talk: Predicting the Conformational Flexibility of Antibody and T-cell Receptor CDRs |
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Katrina Black, UCSF
Short Talk: Improving Cryo-EM of Vesicle-Embedded Membrane Proteins: A Machine Learning Pipeline for Lipid Bilayer Subtraction |
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| 9:30–9:50 AM |
Coffee Break |
Longs Peak Foyer |
| 11:30–1:00 PM |
Poster Setup |
Shavano/Torreys Peaks |
| 11:30–2:30 PM |
On Own for Lunch |
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| 1:00–10:00 PM |
Poster Viewing |
Shavano/Torreys Peaks |
| 2:30–4:30 PM |
Symposia Spotlight: New Machine Learning Applications & Improvements |
Grays Peak |
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* Sergey Ovchinnikov, MIT
Session Chair |
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Peter J Kelly, Align to Innovate
Building the Next Alphafold: Creating Public Databases and Benchmarks to Accelerate Machine Learning for Protein Engineering |
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Samuel Eriksson Lidbrink, Stockholm University
Resolving the Conformational Ensemble of a Membrane Protein by Integrating Small-Angle Scattering with Alphafold |
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Henry R Kilgore, Whitehead Institute for Biomedical Research
Protein Codes Promote Selective Subcellular Compartmentalization |
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Elana Simon, Stanford University
Interplm: Discovering Interpretable Features in Protein Language Models Via Sparse Autoencoders |
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Antoine Koehl, UC Berkeley
Deep Models of Protein Evolution |
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Lai Wei, University of Michigan
An Uncertainty-Aware Method for Single-Particle Cryo-Em Data Collection Using Online Feedback |
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Jishnu Das, University of Pittsburgh
Sliding Window Interaction Grammar (Swing): A Generalized Interaction Language Model for Peptide and Protein Interactions |
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Xinyu Gu, UMD
Empowering Alphafold2 for Protein Conformation Selective Drug Discovery with Alphafold2-Rave |
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| 4:30–5:00 PM |
Coffee Available |
Longs Peak Foyer |
| 5:00–6:45 PM |
Applying Protein Structure Prediction at Scale |
Grays Peak |
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Martin Steinegger, Seoul National University
Fast Search Methods to Organize the Structural Protein Universe |
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* Florian Jug, Fondazione Human Technopole
From Content-Aware Denoising to Semantic Unmixing – One Way How AI is Transforming Scientific Image Data Analysis in The Life Sciences |
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Steffen Lindert, Ohio State University
Short Talk: Deep Learning Models for Protein Structure Elucidation from Different Types of Experimental Data |
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Julia Rogers, Columbia University
Short Talk: Machine Learning the Binding Affinities of Protein–Peptide Interactions in Cell Signaling |
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Jing Zhang, University of Texas Southwestern Medical Center
Short Talk: Protein Structure Classification in the Post-Alphafold Era |
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| 7:00–8:00 PM |
Social Hour with Lite Bites |
Shavano/Torreys Peaks |
| 7:05–8:00 PM |
Women in Science Networking Event |
Crestone Foyer |
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Bridget Carragher, Chan Zuckerberg Imaging Institute
Session Chair |
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Elizabeth Kellogg, St. Jude Children's Research Hospital
Session Chair |
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Elizabeth Villa, University of California, San Diego
Session Chair |
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Suliana Manley, École Polytechnique Fédérale de Lausanne
Session Chair |
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| 7:30–10:00 PM |
Poster Session 1 |
Shavano/Torreys Peaks |
| 7:00–8:00 AM |
Breakfast |
Shavano/Torreys Peaks |
| 8:00–11:00 AM |
CryoET/EM and Machine Learning (Joint) |
Longs Peak / Grays Peak |
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* Allison Doerr, Springer Nature
Session Chair |
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Bridget Carragher, Chan Zuckerberg Imaging Institute
Making Cryo-ET Faster, Better, Cheaper |
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* Bronwyn A Lucas, University of California Berkeley
Single Molecule Localization and Structure Probing in Cells |
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Elizabeth Villa, University of California, San Diego
Discovering New Biology with Cryo-ET |
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Elizabeth Kellogg, St. Jude Children's Research Hospital
Structural Insights into CRISPR-Based Genome Editing |
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Yuriy Chaban, Diamond Light Source ltd.
Short Talk: Automated Filtering of Particle Images in Single Particle CryoEM |
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| 9:00–9:20 AM |
Coffee Break |
Longs Peak Foyer |
| 9:20–9:25 AM |
Award Recipient Acknowledgement |
Longs Peak / Grays Peak |
| 11:00–1:00 PM |
Poster Setup |
Shavano/Torreys Peaks |
| 11:00–5:00 PM |
On Own for Lunch |
|
| 1:00–10:00 PM |
Poster Viewing |
Shavano/Torreys Peaks |
| 3:00–4:30 PM |
Career Roundtable (Joint) |
Grays Peak |
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Kate L. White, University of Southern California
Assistant Professor |
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Christina Y Ivashchenko, Novo Nordisk
Director of Scientific Projects |
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John E Mahoney, Cystic Fibrosis Foundation
Head of Stem Cell Biology |
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Ernesto Andrianantoandro, Cell Press
Scientific Editor, Cell Systems |
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| 4:30–5:00 PM |
Coffee Available |
Longs Peak Foyer |
| 5:00–7:00 PM |
Protein Structure and Drug Discovery |
Grays Peak |
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Tian Cai, St. Jude Children's Research Hospital
AI4BIO: Democratizing AI and Empowering Biologists with a Modular, Open-Source AI Toolkit |
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* Stephanie Wankowicz, Vanderbilt University
Decoding Binding Entropy Through Statistical Structural Biology and Conformational Ensembles |
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John M Nicoludis, Genentech
KnotFold: Improving Peptide Structure Prediction with Simulated Coevolution |
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Garegin Papoian, Deep Origin Inc
Short Talk: Building iIn Silico Models Across Biological Scales to Accelerate Drug Discovery |
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Babgen Manookian, City of Hope
Short Talk: Temporally Resolved and Interpretable Machine Learning Models of G-Protein Coupled Receptors |
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| 7:00–8:00 PM |
Social Hour with Lite Bites |
Shavano/Torreys Peaks |
| 7:30–10:00 PM |
Poster Session 2 |
Shavano/Torreys Peaks |
Wednesday, March 26, 2025
| 7:00–8:00 AM |
Breakfast |
Shavano/Torreys Peaks |
| 8:00–10:30 AM |
Machine Learning for Protein Design |
Grays Peak |
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* Esteban Dodero-Rojas, St Jude Research Children's Hospital
Session Chair |
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Amy E. Keating, Massachusetts Institute of Technology
ML Design of Protein-Binding Peptides |
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Possu Huang, Stanford University
Deep Generative Models for Protein Design |
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Bruno Emanuel Correia, École Polytechnique Fédérale de Lausanne
Expanding the Landscape of Structural and Functional Proteins by Computational Design |
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Christopher Snow, Colorado State University
Short Talk: Fusing Motifs for Avid Sensing, Intracellular Reporters, and Crystalline Assemblies |
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Ariel J Ben-Sasson, ZipBio
Short Talk: De Novo Design of High-Affinity Dual-Target Binders for Drug Polypharmacology Augmentation |
|
| 9:00–9:20 AM |
Coffee Break |
Longs Peak Foyer |
| 11:00–5:00 PM |
On Own for Lunch |
|
| 4:30–5:00 PM |
Coffee Available |
Longs Peak Foyer |
| 5:00–6:15 PM |
Machine Learning Methods Proximal to Protein Structure |
Grays Peak |
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* Qian Cong, UT Southwestern
Computing the Human Interactome |
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Charlotte Deane, University of Oxford
Structural Basis of Small Molecule Binding by Machine Learning |
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Jonathan Schwartz, Chan Zuckerberg Imaging Institute
Short Talk: Advancing Particle Identification In Cryo-Electron Tomograms With Deep Learning |
|
| 6:15–6:30 PM |
Meeting Wrap-Up: Outcomes and Future Directions (Organizers) |
Grays Peak |
| 7:00–8:00 PM |
Social Hour with Lite Bites |
Shavano/Torreys Peaks |
| 8:00–9:00 PM |
Cash Bar |
Shavano/Torreys Peaks |
| 8:00–9:00 PM |
Entertainment |
Grays Peak |
