Machine Learning Applied to Macromolecular Structure and Function
Mar 23–26, 2025 | Keystone Resort, Keystone, CO, United States
Scientific Organizers:
Mohammed AlQuraishi, Elizabeth Kellogg and Possu Huang
In Person
On Demand
Mar 23–26, 2025 | Keystone Resort, Keystone, CO, United States
Scientific Organizers:
Mohammed AlQuraishi, Elizabeth Kellogg and Possu Huang
Available Formats:
Supported by:
In Person
On Demand
***Meeting program subject to change.
Available Formats: = In Person = On DemandSunday, March 23, 2025
Fundraising
Booking Function
Merchandise Options
Registration Options
Registration
4:00–8:00 PM
Longs Peak Foyer
Welcome Mixer
6:00–8:00 PM
Longs Peak Foyer
Monday, March 24, 2025
Breakfast
7:00–8:00 AM
Shavano/Torreys Peaks
Welcome and Keynote Address (Joint)
8:00–9:00 AM
Longs Peak / Grays Peak
* Elizabeth Villa, University of California, San Diego
Session Chair
Session Chair
* Mohammed AlQuraishi, Columbia University
Session Chair
Session Chair
Wolfgang P. Baumeister, Max Planck Institute of Biochemistry
Cryo-Electron Tomography or the Power of Seeing the Whole Picture
Cryo-Electron Tomography or the Power of Seeing the Whole Picture
Machine Learning for Protein Structure (Joint)
9:00–11:30 AM
Longs Peak / Grays Peak
* Julia Rogers, Columbia University
Session Chair
Session Chair
Hannah Wayment-Steele, University of Wisconsin-Madison
Have Protein Language Models Learned Dynamics
Have Protein Language Models Learned Dynamics
Sergey Ovchinnikov, MIT
Hacking AlphaFold to Do New Things
Hacking AlphaFold to Do New Things
* Mohammed AlQuraishi, Columbia University
Understanding How AlphaFold Learns
Understanding How AlphaFold Learns
Fabian C Spoendlin, University of Oxford
Short Talk: Predicting the Conformational Flexibility of Antibody and T-cell Receptor CDRs
Short Talk: Predicting the Conformational Flexibility of Antibody and T-cell Receptor CDRs
Katrina Black, UCSF
Short Talk: Improving Cryo-EM of Vesicle-Embedded Membrane Proteins: A Machine Learning Pipeline for Lipid Bilayer Subtraction
Short Talk: Improving Cryo-EM of Vesicle-Embedded Membrane Proteins: A Machine Learning Pipeline for Lipid Bilayer Subtraction
Coffee Break
9:30–9:50 AM
Longs Peak Foyer
Poster Setup
11:30–1:00 PM
Shavano/Torreys Peaks
On Own for Lunch
11:30–2:30 PM
Poster Viewing
1:00–10:00 PM
Shavano/Torreys Peaks
Symposia Spotlight: New Machine Learning Applications & Improvements
2:30–4:30 PM
Grays Peak
* Sergey Ovchinnikov, MIT
Session Chair
Session Chair
Peter J Kelly, Align to Innovate
Building the Next Alphafold: Creating Public Databases and Benchmarks to Accelerate Machine Learning for Protein Engineering
Building the Next Alphafold: Creating Public Databases and Benchmarks to Accelerate Machine Learning for Protein Engineering
Samuel Eriksson Lidbrink, Stockholm University
Resolving the Conformational Ensemble of a Membrane Protein by Integrating Small-Angle Scattering with Alphafold
Resolving the Conformational Ensemble of a Membrane Protein by Integrating Small-Angle Scattering with Alphafold
Henry R Kilgore, Whitehead Institute for Biomedical Research
Protein Codes Promote Selective Subcellular Compartmentalization
Protein Codes Promote Selective Subcellular Compartmentalization
Elana Simon, Stanford University
Interplm: Discovering Interpretable Features in Protein Language Models Via Sparse Autoencoders
Interplm: Discovering Interpretable Features in Protein Language Models Via Sparse Autoencoders
Antoine Koehl, UC Berkeley
Deep Models of Protein Evolution
Deep Models of Protein Evolution
Lai Wei, University of Michigan
An Uncertainty-Aware Method for Single-Particle Cryo-Em Data Collection Using Online Feedback
An Uncertainty-Aware Method for Single-Particle Cryo-Em Data Collection Using Online Feedback
Jishnu Das, University of Pittsburgh
Sliding Window Interaction Grammar (Swing): A Generalized Interaction Language Model for Peptide and Protein Interactions
Sliding Window Interaction Grammar (Swing): A Generalized Interaction Language Model for Peptide and Protein Interactions
Xinyu Gu, UMD
Empowering Alphafold2 for Protein Conformation Selective Drug Discovery with Alphafold2-Rave
Empowering Alphafold2 for Protein Conformation Selective Drug Discovery with Alphafold2-Rave
Coffee Available
4:30–5:00 PM
Longs Peak Foyer
Applying Protein Structure Prediction at Scale
5:00–6:45 PM
Grays Peak
Martin Steinegger, Seoul National University
Fast Search Methods to Organize the Structural Protein Universe
Fast Search Methods to Organize the Structural Protein Universe
* 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
From Content-Aware Denoising to Semantic Unmixing – One Way How AI is Transforming Scientific Image Data Analysis in The Life Sciences
Steffen Lindert, Ohio State University
Short Talk: Deep Learning Models for Protein Structure Elucidation from Different Types of Experimental Data
Short Talk: Deep Learning Models for Protein Structure Elucidation from Different Types of Experimental Data
Julia Rogers, Columbia University
Short Talk: Machine Learning the Binding Affinities of Protein–Peptide Interactions in Cell Signaling
Short Talk: Machine Learning the Binding Affinities of Protein–Peptide Interactions in Cell Signaling
Jing Zhang, University of Texas Southwestern Medical Center
Short Talk: Protein Structure Classification in the Post-Alphafold Era
Short Talk: Protein Structure Classification in the Post-Alphafold Era
Social Hour with Lite Bites
7:00–8:00 PM
Shavano/Torreys Peaks
Women in Science Networking Event
7:05–8:00 PM
Crestone Foyer
Bridget Carragher, Chan Zuckerberg Imaging Institute
Session Chair
Session Chair
Elizabeth Kellogg, St. Jude Children's Research Hospital
Session Chair
Session Chair
Elizabeth Villa, University of California, San Diego
Session Chair
Session Chair
Suliana Manley, École Polytechnique Fédérale de Lausanne
Session Chair
Session Chair
Poster Session 1
7:30–10:00 PM
Shavano/Torreys Peaks
Tuesday, March 25, 2025
Breakfast
7:00–8:00 AM
Shavano/Torreys Peaks
CryoET/EM and Machine Learning (Joint)
8:00–11:00 AM
Longs Peak / Grays Peak
* Allison Doerr, Springer Nature
Session Chair
Session Chair
Bridget Carragher, Chan Zuckerberg Imaging Institute
Making Cryo-ET Faster, Better, Cheaper
Making Cryo-ET Faster, Better, Cheaper
* Bronwyn A Lucas, University of California Berkeley
Single Molecule Localization and Structure Probing in Cells
Single Molecule Localization and Structure Probing in Cells
Elizabeth Villa, University of California, San Diego
Discovering New Biology with Cryo-ET
Discovering New Biology with Cryo-ET
Elizabeth Kellogg, St. Jude Children's Research Hospital
Structural Insights into CRISPR-Based Genome Editing
Structural Insights into CRISPR-Based Genome Editing
Yuriy Chaban, Diamond Light Source ltd.
Short Talk: Automated Filtering of Particle Images in Single Particle CryoEM
Short Talk: Automated Filtering of Particle Images in Single Particle CryoEM
Coffee Break
9:00–9:20 AM
Longs Peak Foyer
Award Recipient Acknowledgement
9:20–9:25 AM
Longs Peak / Grays Peak
Poster Setup
11:00–1:00 PM
Shavano/Torreys Peaks
On Own for Lunch
11:00–5:00 PM
Poster Viewing
1:00–10:00 PM
Shavano/Torreys Peaks
Career Roundtable (Joint)
3:00–4:30 PM
Grays Peak
Kate L. White, University of Southern California
Assistant Professor
Assistant Professor
Christina Y Ivashchenko, Novo Nordisk
Director of Scientific Projects
Director of Scientific Projects
John E Mahoney, Cystic Fibrosis Foundation
Head of Stem Cell Biology
Head of Stem Cell Biology
Ernesto Andrianantoandro, Cell Press
Scientific Editor, Cell Systems
Scientific Editor, Cell Systems
Coffee Available
4:30–5:00 PM
Longs Peak Foyer
Protein Structure and Drug Discovery
5:00–7:00 PM
Grays Peak
Tian Cai, St. Jude Children's Research Hospital
AI4BIO: Democratizing AI and Empowering Biologists with a Modular, Open-Source AI Toolkit
AI4BIO: Democratizing AI and Empowering Biologists with a Modular, Open-Source AI Toolkit
* Stephanie Wankowicz, Vanderbilt University
Decoding Binding Entropy Through Statistical Structural Biology and Conformational Ensembles
Decoding Binding Entropy Through Statistical Structural Biology and Conformational Ensembles
John M Nicoludis, Genentech
KnotFold: Improving Peptide Structure Prediction with Simulated Coevolution
KnotFold: Improving Peptide Structure Prediction with Simulated Coevolution
Garegin Papoian, Deep Origin Inc
Short Talk: Building iIn Silico Models Across Biological Scales to Accelerate Drug Discovery
Short Talk: Building iIn Silico Models Across Biological Scales to Accelerate Drug Discovery
Babgen Manookian, City of Hope
Short Talk: Temporally Resolved and Interpretable Machine Learning Models of G-Protein Coupled Receptors
Short Talk: Temporally Resolved and Interpretable Machine Learning Models of G-Protein Coupled Receptors
Social Hour with Lite Bites
7:00–8:00 PM
Shavano/Torreys Peaks
Poster Session 2
7:30–10:00 PM
Shavano/Torreys Peaks
Wednesday, March 26, 2025
Breakfast
7:00–8:00 AM
Shavano/Torreys Peaks
Machine Learning for Protein Design
8:00–10:30 AM
Grays Peak
* Esteban Dodero-Rojas, St Jude Research Children's Hospital
Session Chair
Session Chair
Amy E. Keating, Massachusetts Institute of Technology
ML Design of Protein-Binding Peptides
ML Design of Protein-Binding Peptides
Possu Huang, Stanford University
Deep Generative Models for Protein Design
Deep Generative Models for Protein Design
Bruno Emanuel Correia, École Polytechnique Fédérale de Lausanne
Expanding the Landscape of Structural and Functional Proteins by Computational Design
Expanding the Landscape of Structural and Functional Proteins by Computational Design
Christopher Snow, Colorado State University
Short Talk: Fusing Motifs for Avid Sensing, Intracellular Reporters, and Crystalline Assemblies
Short Talk: Fusing Motifs for Avid Sensing, Intracellular Reporters, and Crystalline Assemblies
Ariel J Ben-Sasson, ZipBio
Short Talk: De Novo Design of High-Affinity Dual-Target Binders for Drug Polypharmacology Augmentation
Short Talk: De Novo Design of High-Affinity Dual-Target Binders for Drug Polypharmacology Augmentation
Coffee Break
9:00–9:20 AM
Longs Peak Foyer
On Own for Lunch
11:00–5:00 PM
Coffee Available
4:30–5:00 PM
Longs Peak Foyer
Machine Learning Methods Proximal to Protein Structure
5:00–6:15 PM
Grays Peak
* Qian Cong, UT Southwestern
Computing the Human Interactome
Computing the Human Interactome
Charlotte Deane, University of Oxford
Structural Basis of Small Molecule Binding by Machine Learning
Structural Basis of Small Molecule Binding by Machine Learning
Jonathan Schwartz, Chan Zuckerberg Imaging Institute
Short Talk: Advancing Particle Identification In Cryo-Electron Tomograms With Deep Learning
Short Talk: Advancing Particle Identification In Cryo-Electron Tomograms With Deep Learning
Meeting Wrap-Up: Outcomes and Future Directions (Organizers)
6:15–6:30 PM
Grays Peak
Social Hour with Lite Bites
7:00–8:00 PM
Shavano/Torreys Peaks
Cash Bar
8:00–9:00 PM
Shavano/Torreys Peaks
Entertainment
8:00–9:00 PM
Grays Peak
Thursday, March 27, 2025
Departure
12:00–11:59 PM
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