Day 1 - Wednesday, March 6th, 2024
4:00 pm - 5:00 pm: Meeting Check In
5:00 pm - 6:15 pm: Session 1: Protein design with generative AI
Session Chairs: Brian Kuhlman, Dan Kulp
- 5:00 - 5:10: Welcome: Dan Kulp, Brian Kuhlman
- 5:10 - 5:15: Alexander Klenov, CTO & Aidan Tinafar, CEO, Liberum Bio
- Announcement of Protein Design Competition
- 5:15 - 5:50: Gevorg Grigoryan, Generate Biosciences
- "Programmable generative protein design"
- 5:50 - 6:15: Jason Yim, MIT
- "MultiFlow: : A Unifying Model for Multimodal Protein Structure and Sequence Co-generation"
6:15 pm: Dinner on Site
Boston Marriott Cambridge
7:30 - 9:30: Poster Session 1
Day 2 - Thursday, March 7th, 2024
9:00 am - 11:55 am: Session 2 - Structure Prediction
Session Chairs: Minjae Park, Cristina Martina
- 9:00 - 9:25: Richard Shuai, Stanford
- “Hallucinating multiple sequence alignments with AlphaFold2 for predicting multiple conformations”
- 9:25 - 10:00: Rohith Krishna, University of Washington
- “Generalized Biomolecular Modeling and Design with RoseTTAFold All-Atom“
- 9:00 - 9:25: Richard Shuai, Stanford
- 10:00 - 10:30: Break (Snacks and Coffee)
- 10:30 - 11:05: Phil Bradley, Fred Hutch
- "Predicting and designing T cell receptor interactions"
- 11:05 - 11:30: Arielle Tycko, Vrije Universiteit Brussel
- “Deciphering AlphaFold’s Ability to Predict the Energetic Effects of Single Point Mutations”
- 11:30 - 11:55: Zachary Drake
- “DMS-Fold: Incorporating structural information from deep mutational scanning experiments to enhance OpenFold predictions”
- 10:30 - 11:05: Phil Bradley, Fred Hutch
12:00 pm - 2:00 pm: Lunch
On your own
2:00 pm - 9:00 pm: Headshot Sessions
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2:00 pm - 4:50 pm: Session 3 - Antibodies, TCRs and designed antigens
Session Chairs: Daniel Bader, Hope Woods
- 2:00 - 2:35: Vladimir Gligorljevic, Genentech
- "Generative AI for antibody optimization and de novo design"
- 2:35 - 3:10: Joe Watson, Institute for Protein Design, University of Washington
- Title - "A pipeline for de novo antibody design"
- 3:10 - 3:35: Tomoaki Kinjo, UNC
- “Computational design of bispecific T-cell receptors for cancer therapeutics”
- 2:00 - 2:35: Vladimir Gligorljevic, Genentech
- 3:35 - 4:00: Break (snacks)
- 4:00 - 4:25: Helen Eisenach/David Juergens, Institute for Protein Design, University of Washington
- “Methods development for antigen-tailored nanoparticle vaccine design with RFdiffusion”
- 4:25 - 4:50: Mihai Azoitei, Duke University
- “Rational Vaccine Design to Target Conserved Regions of Coronavirus Spike Proteins”
- 4:00 - 4:25: Helen Eisenach/David Juergens, Institute for Protein Design, University of Washington
4:50 pm - 5:55 pm: Session 4 - AI and Biosafety
- 4:50 - 5:15: Jeff Gray (Johns Hopkins University), Alex Rives (Evolutionary Scale), Ian Haydon (University of Washington/Institute for Protein Design)
- "Community principles for the responsible use of AI in protein design"
- 5:15 - 5:35: Samuel Curtis, Nick Randolph, Matt Schultz
- "A Glance at the Intersection of LLMs and Biological Design Tools"
- 5:35 - 5:55: Jonas Sandbrink (UK Department for Science, Innovation and Technology, AI Safety Insitute)
- 4:50 - 5:15: Jeff Gray (Johns Hopkins University), Alex Rives (Evolutionary Scale), Ian Haydon (University of Washington/Institute for Protein Design)
6:00 pm - 7:30 pm: Dinner on Site + Biosafety Discussion Tables
Boston Marriott Cambridge
7:30 pm - 9:30 pm: Poster Session 2
Day 3 - Friday, March 8th, 2024
9:00 am - 11:55 am: Session 5 - Peptide and Protein Design
Session Chairs: Odessa Goudy, Sebastian Swanson)
- 9:00 - 9:25: Daniella Pretorius, Imperial College
- “Into the Darkness: Exploring and Expanding the Solenoid Protein Universe”
- 9:25 - 10:00: Amy Keating, MIT
- “Putting sequences on backbones and putting peptides on proteins“
- 9:00 - 9:25: Daniella Pretorius, Imperial College
- 10:00 - 10:30: Break
- 10:30 - 10:55: Patrick Finneran, Menten AI
- “Design of Drug-like Cyclic Peptides Using Generative AI”
- 11:05 - 11:30: Kevin Yang, Microsoft
- “Deep learning for protein engineering“
- 11:30 - 11:55: Amy Guo, UCSF
- “Engineering Ca2+-modulated local conformational dynamics”
- 10:30 - 10:55: Patrick Finneran, Menten AI
11:55 am - 1:15 pm: Lunch On Site
Boston Marriott Cambridge
1:15 pm - 3:00 pm: Session 6 - Protein design applications
Session chairs: Fatima Hitawala, Amelia McCue
- 1:15 - 1:40: Emily Wrenbeck, Gingko Bioworks
- “Labels are all you need - functional enzyme discovery & engineering with applied ML & Foundry-scale data”
- 1:40 - 2:15: Chris Bahl
- "Better medicines, created rapidly through de novo miniprotein design"
- 2:15 - 2:40: Vidar Sarma, Rutgers
- "Profiling, predicting and designing viral 3C protease substrate specificity using high-throughput yeast surface display"
- 2:40 - 2:50: Closing remarks
- 1:15 - 1:40: Emily Wrenbeck, Gingko Bioworks
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