Session Chair: Amrita Nallathambi and Sudeep Sarma

• • 9:00 - 9:30: David La
    • Invited: "De novo Binder Design with AlphaProteo"
  • 9:30 - 9:45: Jesse Durham
  • • "Domain Parser for AlphaFold Models using Artificial Intelligence (DPAM-AI)"
  • 9:45 - 10:00: Zachary Drake
    • "DMS-Fold: Deep-Learning Structure Elucidation from Single-Mutant Deep Mutational Scanning"
  • 10:00 - 10:15: Feng Zhang
    • "MetalNet2: an enhanced server for predicting metal-binding sites in proteomes"

10:15 - 10:30: Break (snacks and coffee)

Session Chair: Huong Kratochvil and Fabian Liessmann

• • 10:30 - 10:45: Joseph Lubin
    • "Filling Gaps and Building Missing Loops in Protein Crystal Structures with TandemFill"
  • 10:45 - 11:00: Roland Dunbrack
    • "What's wrong with AlphaFold's ipTM metric and how to fix it"
  • 11:00 - 11:15: Andrew Muenks
    • "Automated identification of small molecules in cryo-electron microscopy data with density- and energy-guided evaluation"
  • 11:15 - 11:30: Akshaya Narayanasamy
    • "Ion mobility guided Monte Carlo-based docking pipeline for predicting protein complexes"
  • 11:30 - 12:00: Gabriele Corso & Jeremy Wohlwend
    • Invited: "Boltz-1: Democratizing Biomolecular Interaction Modeling"

Explore career options with organized lunches or network on your own.

PIs and industry attendees looking to recruit new group members can self-identify to organize an ad hoc lunch. Use the restaurant list to scope a place out.

Generate: Biomedicine is sponsoring a career lunch. Check the Nunify app for details and to sign up.

Session Chair: Malcolm Wells and Yehlin Cho

• • 2:00 - 2:15: Aransa Griñen
    • "Designing novel PET-degrading enzymes using deep-learning"
  • 2:15 - 2:30: Katerina Blejec
    • "Probing the spontaneous posttranslational modification of de novo designed miniproteins at extreme temperatures"
  • 2:30 - 3:00: George Church
    • Keynote: "Beyond protein rocks: MLML for allostery, viral capsids, ribosomes, & biocontainment"
  • 3:00 - 3:15: Mariana Carletti
    • ProteinMPNN-Driven Design of Functional PI-PLC Variants: A Combined Computational and Experimental Approach
  • 3:15 - 3:30: Gaohua Liu
    • Characterization of Antibody Allostery: A Platform for Protein Design and Drug Discovery

3:30 - 4:00 Break (snacks and coffee)

Session Chair: Nick Randolph and Cesar Ramirez

• • 4:00 - 4:30: Peter Kim
    • Keynote: "Protein language models for understanding and guiding evolution"
  • 4:30 - 4:45: Brian Pierce
    • "Expanding the TCR3d Database: Structures, Affinities, and Implications for Modeling and Design of Immune Recognition"
  • 4:45 - 5:00: Shayana Saravanakumar
    • "Benchmarking AlphaFold3 and related methods for TCR-pMHC structure prediction and identifying score cutoffs indicative of high-quality models"
  • 5:00 - 5:15: Helder Ribeiro
    • "Exploring the potential of structure-based deep learning approaches for T cell receptor design"
  • 5:15 - 5:30: Malcolm Wells
    • Evolution of functionally important conformational changes in an ancient protein fold

5:30 - 5:45 Bio-break/Bathroom break

Session Chair: Helder Riberio and Joseph Lubin

• • 5:45 - 6:00: Andreas Petrides
    • "Folding in the Web: Bringing Foldit to your Browser"
  • 6:00 - 6:15: Sam DeLuca
    • "Levitate Bio: Supporting RosettaCommons through accessible and usable protein engineering tools"
  • 6:15 - 6:30: Jack Maguire
    • "Debugging a Dangerous PyRosetta Liability in the NotResidueSelector and Other Classes from the C++-to-Python Binding Process"
  • 6:30 - 6:45: Christopher Moth
    • "VUStruct: High Throughput Structural Biology for the Clinic"

Boston Marriott Cambridge