RosettaCon on August 5-9, 2024

Watch the Recorded Talks

Summer RosettaCon 2025

Day

Hour

Minute

Second

Summer RosettaCon Schedule

All Times Subject to Change

Locations for the following events:

Main conference occurs at The Lodge, Suncadia Resort
Breakfast - Rialto and Prefunction Space
Lunch - Tent (near the driving range...)
Dinner - Roslyn Meadow
Poster Sessions - Rialto & Owens Ballrooms
Mix and Mingle - Roslyn Meadow

Jump to...

Monday
Tuesday
Wednesday
Thursday
Friday

Day 1 - Monday, August 5th, 2024

9 am - 2 pm : Shuttles from SeaTac/UW

See the conference information page for details. Meet your shuttle at Baggage Claim 16.

4 pm - 5 pm : Check-in & Badge Pick-up

After checking in at The Lodge, use Google Maps and the address to find your unit.

5:00 pm : Welcome Session

- Welcome remarks: Gabe Rocklin and Gaurav Bhardwaj
- Code of Conduct: JEDI Committee
- Committee updates
- CoMotion update

5:45 pm : Keynote Talk - David Baker - Design of Protein Holliday Junctions

6:30 pm : Dinner

7:30 pm : Poster Session

9:00 pm : Mix and mingle

- Drinks and Snacks
- Pub and Lawn Games
- Ends at 11:30

Day 2 - Tuesday, August 6th, 2024

7:00 am : Breakfast

8:45 am : Parallel Talk Session 1A - Enzyme Design and Engineering (Part I)

Session Chair: Owen Rogers

- 8:45 - 9:05 : Emma Luu
  - Engineering Escherichia coli Pyruvate Metabolism to Generate Noncanonical Reducing Power
- 9:05 - 9:25 : Samuel Garfinkle
  - Results of Winter Protein Design Games 2024
- 9:25 - 9:45 : Sam Pellock and Anna Lauko
  - Design of multistep enzymes

8:45 am : Parallel Talk Session 1B - Proteins with multiple conformational states

Session Chair: Kathryn Shelley

- 8:45 - 9:05 : Dominic Grisingher
  - De novo designing proteins with two conformational states for application in engineering synthetic signaling
- 9:05 - 9:25 : Tomiris Mulikova
  - Designing de novo allostery using Deep Learning methods
- 9:25 - 9:45 : Ajasja Ljubetič
  - Single molecule tracking of a completely de novo designed random protein walker

9:45 am : Morning Break

10:05 am : Parallel Talk Session 2A - Designing small-molecule binding proteins

Session Chair: Linna An

- 10:05 - 10:25 : Hyunjun Yang
  - De Novo Protein Design of Herbicide-Binding Proteins
- 10:25 - 10:45 : Yuda Chen
  - From a Generalist to Specialists: De Novo Protein Design for Ligand Binding and Catalysis

10:05 am : Parallel Talk Session 2B - De novo Antibody Design

Session Chair: Donovan Vincent Jr.

10:05 - 10:25 : Russel Ault
- De novo antibody design with fine-tuned RFdiffusion for pediatric oncology immunotherapeutics
10:25 - 10:45 : Rob Alberstein
- AAA: Structural bioinformatics in Rosetta - Insights into antibody structure & sequence

11:00 am : Small group introductions

Introduce yourself to others and give a 5-minute flash talk about research and dream goals. Group assignments - Locations

12:10 pm : Lunch

1:30 pm : Parallel Talk Session 3A - Protein Design Applications: Therapeutics and Beyond

Session Chair: Savannah McBride

- 1:30 - 1:50 : Seong Guk Park and Jung-Un Park
  - Engineering CRISPR-Associated Transposon for Enhanced Activity and Precision using High-throughput Screens and Computational Protein Design
- 1:50 - 2:10 : Nate Ennist
  - De novo protein design for enhanced photosynthesis
- 2:10 - 2:30 : Susana Vazquez Torres
  - Design of anti-venoms

1:30 pm : Parallel Talk Session 3B - New Methods and Benchmarking (Part I)

Session chair: Yensi Flores Bueno

- 1:30 - 1:50 : Sergey Ovchinnikov
  - Scalable protein design using optimization in a relaxed sequence space
- 1:50 - 2:10 : Minjae Park
  - Comparison of AlphaFold3 and massive sampling for modeling antibody and T cell receptor recognition
- 2:10 - 2:30 : Zhuofan Shen
  - Benchmarking Rosetta and LigandMPNN in Multi-State Design of Stereoselective Hemoprotein Cyclopropanases

2:30 pm : Future of Rosetta discussions (and break begin)

3:15 pm : Break with activities

4:30 pm : Parallel Talk Session 4A - Generative Deep Learning for Protein Modeling and Design

Session Chair: Alex Li

- 4:30 - 4:50 : Jeffrey Ruffolo
  - Steering protein language models for functional protein design
- 4:50 - 5:10 : Yo Akiyama
  - Recapitulating natural co-evolutionary statistics using deep generative models
- 5:10 - 5:30 : Possu Huang
  - Protpardelle: an all-atom protein generative model

4:30 pm : Parallel Talk Session 4B - Structure-guided Vaccine Design

Session Chair: Sanela Rankovic

- 4:30 - 4:50 : Mark Langowski
  - Design and characterization of germline-targeting vaccines for P. falciparum malaria
- 4:50 - 5:10 : Cristina Elisa Martina
  - Glycan masking in vaccine design against influenza virus
- 5:10 - 5:30 : Daniel Ellis
  - Designing stabilized vaccines in the face of antigenic variability

5:40 pm : Group Photo

6:00 pm : Dinner

7:30 pm : Keynote Talk - Dave Savage - Mapping the biochemical landscape of CO2 fixation

Rialto Ballroom

Session Chair: Xinru Wang

8:30 pm : Poster Session 2

10:00 pm : Mix and Mingle

- Drinks and Snacks
- Pub and Lawn Games
- Ends at 11:30

Day 3 - Wednesday, August 7th, 2024

7:00 am : Breakfast

8:45 am : Deep Learning Tutorial A - Binder Design with RFdiffusion and ProteinMPNN

- Preetham Venkatesh
- Xinru Wang

8:45 am : Deep Learning Tutorial B - Optimizing language models with your data

- Sergey Ovchinnikov
  - SaprotHub

9:45 am : Break

10:05 am : Parallel Talk Session 5A - Enzyme Design and Engineering (Part II)

Session Chair: Christopher Shelby

- 10:05 - 10:25 : Alexander Kehl
  - Understanding the Evolution of Rubisco Oligomeric State
- 10:25 - 10:45 : Markus Braun
  - De novo enzyme design by artificial motif library scaffolding

10:05 am : Parallel Talk Session 5B - New Methods and Benchmarking (Part II)

Session Chair: Sudeep Sharma

- 10:05 - 10:25 : Yehlin Cho
  - Enhancing Protein Design Robustness through Noise-Informed Sequence Design
- 10:25 - 10:45 : Levitate Bio (Sam DeLuca and Karen Khar)
  - Meet Levitate: Making Rosetta Accessible and Profitable

10:50 am : JEDI Keynote : Carol Muller - Understanding and Approaching Mentoring

RosettaCon Mentoring Tip Sheet

12:20 pm : Lunch

1:40 pm : Parallel Talk Session 6A - Designing peptides and small molecules (Part I)

Session Chair: Gizem Gokce

- 1:40 - 2:00 : Ora Schueler-Furman
  - One shot design of potent and specific inhibitor of PP2A phosphatase regulatory subunit B55 and its use for the study of cellular regulation
- 2:00 - 2:20 : Stephen Rettie
  - Computational design of accurate, high-affinity macrocyclic peptide binders using deep learning models
- 2:20 - 2:40 : John Karanicolas
  - Generative AI to design small molecules

1:40 pm : Parallel Talk Session 6B - Large scale PPI prediction and measurement

Session Chair: Sara Volz

- 1:40 - 2:00 : Ian Humphreys
  - Proteome-wide protein-protein interactions revealed through deep learning and coevolution
- 2:00 - 2:20 : Jing Zhang
  - Computed cancer interactome explains the effects of somatic mutations in cancers
- 2:20 - 2:40 : Samantha Fischer
  - Characterization of physicochemical factors responsible for protein complex stability

2:40 pm : LONG Break with group activities

Archery, axe throwing, and more

6:00 pm : Dinner

7:30 pm : Keynote - Polly Fordyce - Leveraging microfluidics for high-throughput and quantitative protein purification and characterization

Session Chair: Jason Zhang

8:30 pm : Poster Session

10:00 pm : Mix and Mingle

- Drinks and Snacks
- Pub and Lawn Games
- Ends at 11:30

Day 4 - Thursday, August 8th, 2024

7:00 am : Breakfast

8:45 am : Parallel Talk Session 7A - Designing Functional Proteins

Session Chair: Stephanie Crilly

- 8:45 - 9:05 : Zibo Chen
  - A synthetic protein-level neural network in mammalian cells
- 9:05 - 9:25 : Philipp Huettemann
  - Engineering synthetic cluster signaling hubs using de novo protein design
- 9:25 - 9:45 : Shawn Yu
  - Trispecific T-cell engagers with bivalent TCR-based antigen targeting through orthogonal interface design

8:45 am : Parallel Talk Session 7B - Multiple States and Allostery

Session Chair: Andra Campbell

- 8:45 - 9:05 : Gaetano Montelione
  - Hidden structural states of proteins revealed by conformer selection with AlphaFold-NMR
- 9:05 - 9:25 : Camila Neira
  - Single-position masking as an strategy to explore the conformational landscape of proteins in AlphaFold2
- 9:25 - 9:45 : Belen Sundberg
  - Elucidating the allosteric regulation of PFK-1

9:45 am : Break

10:05 am : Parallel Talk Session 8A - Design methods for oligomers and immunogens

Session Chair: Thomas Schlichthaerle

- 10:05 - 10:25 : Chelsea Fries
  - Breaking local symmetry in oligomers with constrained backbone reconstruction
- 10:25 - 10:45 : Karen Juliana Gonzalez Restrepo
  - Engineering HA variants using consensus-based protein design

10:05 am : Parallel Talk Session 8B - High-throughput measurements

Session Chair: Linna An

- 10:05 - 10:25 : Sarah Fahlberg
  - Systematic evaluation of ML-based protein design methods for peptide discovery via peptide array characterization
- 10:25 - 10:45 : Cydney Martell
  - The determinants of aggregation in small protein domains

11:00 am : Career Panels

- Choosing Graduate School and Postdoc Positions - Fire pit
  - Kathryn Shelley, David Ding, Justin Miller, Steph Crilly
- Careers at Small Companies - Rialto
  - Daniel Smith, Adva Yeheskel, Alfredo Quijano-Rubio, Yu-Ru Lin
- Careers at Large Companies - Owens
  - Rob Alberstein, Erin Yang, Evan Mirts, BoRam Lee
- Careers in Academia and Finding Academic Positions - Miller
  - Cameron Glasscock, Hyunjun Yang, Anum Glasgow, Kevin Drew

12:10 pm - 1:30 pm: Lunch

1:30 pm : Parallel Talk Session 9A - Advances in Membrane Protein Design

Session Chair: Moritz Ertelt

- 1:30 - 1:50 : Ljubica Mihaljevic
  - Solubilization of Membrane Proteins using de novo WRAPs
- 1:50 - 2:10 : Chen Zhou
  - De novo design of a voltage-gated anion channel
- 2:10 - 2:30 : Jingyi Zhu
  - De novo designed transmembrane proteins activating bright fluorescence in membranes

1:30 pm : Parallel Talk Session 9B - Advances in High-throughput Screening

Session Chair: Justin Miller

- 1:30 - 1:50 : Shlomo Yakir Hoch Cohen
  - GGAssembler: precise and economical design and synthesis of combinatorial mutation
- 1:50 - 2:10 : Zhiyuan Yao
  - Enhancing Miniprotein Binder Screening with mRNA Display
- 2:10 - 2:30 : Christopher Shelby
  - Enhancing tyrosinase’s catalytic efficiency and selectivity through substrate recruitment

2:30 pm : Break with Activities

1000 steps with River Viewing

3:30 pm : REU Intern meeting

- 3:30 - 5:00
- For participants of the Rosetta Commons REU Intern program, their faculty sponsors, and mentors

4:00 pm : Scientific breakout groups

Discussion of interesting scientific topics. Topic list - Locations

5:15 pm : Parallel Talk Session 10A - Designing target-binding proteins

Session Chair: Thomas Schlichthaerle

- 5:15 - 5:35 : Jason Zhang
  - De novo design of Ras isoform selective binders by targeting their highly charged C-terminus
- 5:35 - 5:55 : Andrew McShan
  - De Novo Design of Antagonists Targeting Bacterial Secretion System Assembly

5:15 pm : Parallel Talk Session 10B - Designing peptides and small molecules (Part II)

Session Chair: Guangfeng Zhou

- 5:15 - 5:35 : Andrew Powers
  - Continuous structural space autoencoder for cyclic peptide backbone design
- 5:35 - 5:55 : Matthew O'Meara
  - ChemPile: aggregating diverse bioactive data for training chemical foundation models

6:00 pm : Dinner

7:30 pm : Keynote Talk - Mike Jewett - Accelerating protein design with cell-free systems

Session Chair: Kosuke Seki

8:30 pm : PI Meeting

Smores, Smores, Snores!

8:30 pm : Mix and Mingle behind the Inn

- Drinks and Snacks
- Pub and Lawn Games
- Ends at 11:30

Day 5 - Friday, August 9th, 2024

7:00 am : Breakfast

9:00 am : Depart to Airport or Activities

Plan for a day of hiking, biking, rafting, or other activity with your fellow conferencegoers.

Some people might stay back and hang out during the day.

Shuttles back to Seattle running all day long.

9:00 am : Shuttles leave for SEATAC/Seattle

Questions or Comments? Please Contact Us

RosettaCon is a place where Rosetta Commons member laboratories and invited guests share their latest experimental and computational research breakthroughs in macromolecular engineering and structure prediction.

For more information about Rosetta Commons please go to the Rosetta Commons Website