Schedule

Day 1 - Wednesday, February 26th, 2025

• • 4:00 pm - 5:00 pm: Meeting Check In

  • 5:00 pm - 5:15 pm: Welcome
    Scientific Organizers: Anum Glasgow & Sergey Ovchinnikov

  • 5:15 pm - 6:20 pm: Session 1: Protein design with generative AI
    Session Chair: Alena Khmelinskaia and Colby Agostino

    • 5:15 - 5:30: Amrita Nallathambi

      • "Improving experimental success rates of de novo protein design through extensive iterative optimization"

    • 5:30 - 5:45: Bryce Johnson

      • "Non-Native Enzyme Engineering with a Biophysical Protein Language Model"

    • 5:45 - 6:00: Alex Li

      • • "ProteinZen: combining latent and SE(3) flow matching for all-atom protein generation"

    • 6:00 - 6:20: David La

      • • Invited: "De novo Binder Design with AlphaProteo"

  • 6:30 pm - 7:30 pm : Dinner on Site + JEDI Discussion Table

    • • • Boston Marriott Cambridge

  • 7:30 pm - 9:30 pm: Poster Session 1

Day 2 - Thursday, February 27th, 2025

• 9:00 am - 10:15 am: Session 2 - Structure Prediction I
  Session Chair: Amrita Nallathambi and Sudeep Sarma

  • • 9:00 - 9:30: Debora Marks

      • Keynote: "How can AI accelerate therapeutic protein design?"

    • 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)

• 10:30 am - 11:50 am: Session 3 - Structure Prediction II
  Session Chair: Huong Kratochvil

  • • 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 - 11:50: Gabriele Corso

      • Invited: "Boltz-1: Democratizing Biomolecular Interaction Modeling"

• 11:50 pm - 12:00 pm: Group Photo

• 12:00 pm - 2:00 pm: Lunch

  • 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.

• 2:00 pm - 3:30 pm: Session 4 - Protein design applications I
  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)

• 4:00 pm - 5:30 pm: Session 5 - Protein-protein interactions
  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

• 5:45 pm - 6:45 pm: Session 6 - Next-Generation Tools for Computational Structural Biology
  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"

• 6:45 pm - 8:00 pm: Dinner on Site + Biosafety Discussion Tables

  • Boston Marriott Cambridge

• 8:00 pm - 10:00 pm: Poster Session 2

Day 3 - Friday, February 28th, 2025

• 9:00 am - 10:30 pm: Session 7 - Stability and conformational changes in proteins
  Session Chair: Jordan Hoff and Zhidian Zhang

  • • 9:00 - 9:30: Pilar Cossio

      • Keynote: "Probing conformational ensembles and thermodynamics using cryo-electron microscopy images"

    • 9:30 - 9:45: Meagan MacDonald

      • "Changes in Photophysical Characteristics of DFHBI Fluorophore Bound to Mini Fluorescence Activating Proteins Using 19F NMR"

    • 9:45 - 10:00: Alena Khmelinskaia

      • "(First) Tales of Dynamic Protein Assemblies"

    • 10:00 - 10:15: Yehlin Cho

      • "Absolute folding stability prediction for small protein domains"

    • 10:15 - 10:30: Felipe Engelberger

      • "A recipe for maximizing AF2 conformational exploration while preserving high model quality"

    • 10:30 - 10:45: Bhoomika Basu Mallik

      • "Towards predicting oligomorphism in de novo designed protein assemblies"

• 10:45 - 11:15: Break (snacks & coffee)

• 11:15 am - 12:00 pm: Session 8 - Protein design applications II
  Session Chair: Mariana Carletti and Sam DeLuca

  • • 11:15 - 11:30: Colby Agostino

      • "Leveraging deep learning-based protein design to scaffold the HIV-1 envelope trimer base"

    • 11:30 - 11:45: Rommel Granja Travez

      • "Machine Learning-Driven Optimization of MHETase for Enhanced PET Biodeconstruction"

    • 11:45 - 12:00: Huong Kratochvil

      • "Protons on the move: Design of selective, functional proton channels"

• 12:00 pm - 12:15 pm: JEDI Discussion

  • Led by Firas Khatib, JEDI Chair & Jeff Gray (Rosetta Commons Director)

• 12:15 pm - 1:45 pm: Lunch On Site

  • Boston Marriott Cambridge

• 1:45 pm - 3:15 pm: Session 9 - Protein design for peptides, small molecules, and minibinders
  Session Chair: Jack Maguire

  • • 1:45 - 2:00: Mike Nichols

      • Massively Parallel Discovery and In Vivo Validation of Tissue-targeting Protein Minibinders Using RFDiffusion and mCode Multiplexing

    • 2:00 - 2:15: Fengzhang Wang

      • "Rational Design of Covalent Peptide Binders"

    • 2:15 - 2:30: Parisa Hosseinzadeh

      • "How to make cyclic peptides even better"

    • 2:30 - 2:45: Fabian Liessmann

      • "Hederagenin is a Highly Selective Antagonist of the Neuropeptide FF Receptor 1 that Reveals Mechanisms for Subtype Selectivity"

    • 2:45 - 3:00: Benjamin Fry

      • "Design of small molecule binding proteins using LASErMPNN"

• 3:00 pm - 3:15 pm: Closing Remarks

• 4:00 pm - 6:00 pm: Happy Hour sponsored by Pillar VC

  • Unwind and socialize with colleagues and collaborators at this Happy Hour hosted by Pillar VC. Sign-up is required and accessible using the Nunify app.