Day 1: Tuesday, August 8th
8:45am Van departures from Lander Hall (for out of Seattle area attendees)
11:30am-2:00pm Lunch (Kingfisher)
- 1:00-1:50pm Rosetta Commons Executive Board Meeting (Woodpecker)
- 1:00-1:50pm Industry Participants Meet & Greet (Flicker)
2:00-2:30pm Session 0 (Chapel & video streaming to Woodpecker)
- 2:00-2:10pm Welcome by the organizers
- 2:10-2:20pm Jeff Gray, JHU, Code of Conduct
- 2:20-2:30pm Dennis Hanson, UW CoMotion, RosettaCommons Annual Review
2:40-4:00 pm Session 1A (Chapel)
Broad Topic: Scoring Functions
Chair: Lars Malmström
- 2:40-3:00pm Rebecca Alford, JHU, What's in Pandora's box? A guide to the Rosetta energy function
- 3:00-3:20pm Jens Meiler, Vanderbilt, A Holistic Approach to Partial Covalent Interactions in Protein Structure Prediction and Design with Rosetta
- 3:20-3:40pm Frank Dimaio, UW, Advances in Rosetta Energy Function Optimization
- 3:40-4:00pm Hahnbeom Park, UW, Protein homology model refinement with deep conformational sampling in energy landscape
2:40-4:00 pm Session 1B (Woodpecker)
Broad Topic: Sampling Methods
Chair: Dominik Gront
- 2:40-3:00pm Colin Smith,Wesleyan U, Modeling NOE Buildup Data with Structural Ensembles
- 3:00-3:20pm Xingjie Pan, UCSF, Reconstruction of protein geometries with fragment insertion and robotics-inspired sampling
- 3:20-3:40pm Justin Seffernick, Ohio State, Modeling Surface Induced Dissociation to Improve Protein-Protein Docking
- 3:40-4:00pm Ryan Pavlovicz, UW, Efficient consideration of coordinated water molecules improves computational protein-protein and protein-ligand docking
4:00-4:20pm Coffee Break (Salmon Gallery) & Rooms Check In
4:20-5:00 pm Session 2A (Chapel)
Broad Topic: Design of large molecular assemblies
Chair: Ingemar Andre
- 4:20-4:40pm Neil King, UW, Design of self-assembling protein nanomaterials for medical applications
- 4:40-5:00pm Joseph Yesselman, Stanford, Automated Design of Asymmetric Three-Dimensional RNA Structures and Machines at Near-Atomic Accuracy
4:20-5:00 pm Session 2B (Woodpecker)
Broad Topic: Protein Design Strategies
Chair: Brian Kuhlman
- 4:20-4:40pm Scott Boyken, UW, Hydrogen bond network-mediated specificity and protein logic
- 4:40-5:00pm Shipra Malhotra, FCCC, What Fraction of the Protein-Protein Interaction Space is Druggable by Allosteric Inhibition?
5:00-5:30pm Rooms Check-in
5:30-7:00pm Dinner (Kingfisher)
7:30-8:15pm Keynote Session 1 (Chapel & video streaming to Woodpecker)
Chair: TBD
- David Baker, UW, TBA
8:30pm Poster Session 1 (Quail and Tadpole)
9:30pm Open Bar and Alternative Activities
9:30 pm Icebreakers and Team Building Challenges (Flicker)
10:00 pm Annual Carcassonne Tournament, Round 1
Day 2: Wednesday, August 9th
7:30-9:00am Breakfast (Kingfisher & Icicle Village)
9:00-10:20am Session 3A (Chapel)
Broad Topic: Scoring Functions II
Chair: Charlie Strauss
- 9:00-9:20am Rijhu Das, Stanford, Partition functions for RNA folding transitions with Rosetta
- 9:20-9:40am Rich Bonneau, NYU, Hybrid scoring functions: a multitude of approaches to mixed energy functions
- 9:40-10:00am Jonathan Weinstein, Weizmann, Calibrating an energy function for membrane protein design and modeling
- 10:00-10:20am Andrew Leaver-Fay, UNC, A Non-pairwise-decomposable hydrogen bonding function
9:00-10:20am Session 3B (Woodpecker)
Broad Topic: DNA/RNA & Large Molecular Complexes
Chair: Vatsan Raman
- 9:00-9:20am Possu Huang, Stanford, Structure modeling of the bacteriophage phi29 DNA packaging motor
- 9:20-9:40am Nancy Hernandez, Rutgers, Computational Design of a Stimulus-responsive Fractal-like Supramolecular Enzyme Assembly for Biodegradation
- 9:40-10:00am Andrew Watkins, Stanford, Achieving atomic accuracy in blind RNA structure prediction
- 10:00-10:20am Kalli Kappel, Stanford, Towards automated coordinate completion of large RNA-protein machines
10:20-10:40am Coffee Break (Salmon Gallery)
10:40am-12:00pm Topic-Focused Break-Out Discussions
- Rosetta 101 - Tutorial for beginners
- Speaker: Vikram Mulligan, UW
- Protein-Protein Interface Design (Woodpecker)
- Moderator: Tim Whitehead
- Chalk talk: Hayretin Yumerefendi, UNC, Benchmarking protocols for predicting protein-protein binding affinity
- Chalk talk: David Nannemann, EMD, Antibody optimization and interface design
- Structure Prediction (Dipper)
- Moderator: Nik Sgourakis
- Chalk talk: Stephanie Kim, OSU, Predicting Intrinsically Disordered Regions of Protein
- Chalk talk: Chris Bystrof, RPI, How well backrub, KIC and MD work in predicting backbone atom shifts
- Protein-Small Molecule Prediction and Design (Flicker)
- Moderator: John Karanicolas
- Chalk talk: Jake Khowsathit, FCCC, Computational design of ligand-activated antibodies
- Membrane Proteins (Nuthatch)
- Moderator: Erik Procko
- Chalk talk: Phuong Nguyen, UCDavis, Sodium conduction through Rosetta model of voltage gated sodium channel
- Chalk talk: Aiyana Emigh, UCDavis, Modeling rNav1.2-Conotoxin GVIIJ Binding
- Energy Function (Grotto Pub)
- Moderator: Jim Havraneck
- Chalk talk: Jim Havraneck, WU, Multipole Electrostatics in Rosetta
- Chalk talk: Douglas Renfrew, Simons, Two-Component Reference Energy for the Design of Proteins and Foldamers
- Rosetta GUIs (Salmon Gallery Terrace)
- Moderator: Seth Cooper
- Chalk talk: Lucas Nivon, Cyrus, TBD
- RNA & DNA (Kingfisher Terrace)
- Moderator: Rhiju Das
- Chalk talk: Marcin Magnus, Warsaw, RNA 3D Structure Prediction Using Multiple Sequence Alignment Information
- Integrative modeling (Playbarn)
- Moderator: Steffen Lindert
- Chalk talk: George Kuenze, Vanderbilt, A general framework for protein structure prediction and modeling with paramagnetic NMR restraints
- Chalk talk: Melanie Aprahamian, Ohio State, Incorporation of Mass Spectrometry Covalent Labeling Experimental Data into Rosetta Scoring Function
12:00pm-2:00pm Lunch (Kingfisher) and Community Discussion Breakouts
- 12:00-1:00pm Discussion Session I, Supporting diversity in the Rosetta Community, Led by Una Nattermann
- 1:00-2:00pm Discussion Session II, Supporting Diversity in the Rosetta Community, Led by Rebecca Alford
2:00-3:00pm Session 5A (Chapel)
Broad Topic: Enzyme Design I
Chair: Florian Richter
- 2:00-2:20pm Alex Zanghellini & Jacob Bale, Arzeda, Scaling Enzyme and Pathway Design
- 2:20-2:40pm Manasi Pethe, Rutgers, Illuminating the protease-substrate specificity landscape for the HCV NS3 protease using computation and deep sequencing methods
- 2:40-3:00pm Steve Bertolani, UCDavis, Modeling enzyme active sites
2:00-3:00pm Session 5B (Woodpecker)
Broad Topic: Protein Therapeutics
Chair: Vanita Sood
- 2:00-2:20pm Bill Schief, TSRI, Germline-targeting vaccine design
- 2:20-2:40pm Christopher Bahl, UW, De novo design of antivirulence therapeutics based on genetically encodable, hyperstable constrained peptides
- 2:40-3:00pm Amandeep Sangha, Vanderbilt, Epitope focused vaccine design against Ebola virus
3:00-3:30pm GROUP PICTURE near Kingfisher entrance followed by Coffee Break (Salmon Gallery)
3:30-4:30pm Session 6A (Chapel)
Broad Topic: Rosetta GUIs
Chair: Jordan Billups
- 3:30-3:50pm Steven Lewis, Cyrus, Cyrus Biotechnology update
- 3:50-4:10pm Seth Cooper, Northeastern, Foldit
- 4:10-4:30pm Aaron Virshup, Autodesk, Full Stack Molecular Modeling: building open platforms for interoperable, reproducible, and extensible molecular modeling
3:30-4:30pm Session 6B (Woodpecker)
Broad Topic: Docking
Chair: Deanne Sammond
- 3:30-3:50pm Brian Pierce, UM, Modeling and design of T-cell receptors
- 3:50-4:10pm Shourya Sonkar Roy Burman, JHU, Efficient flexible-backbone protein docking using motif scoring of large conformational ensembles
- 4:10-4:30pm Mainak Guha Roy, VIB, Discovering novel short linear motifs based on peptide-protein docking
4:30-4:50pm Coffee Break (Salmon Gallery)
4:50-5:30pm Session 7A (Chapel)
Broad Topic: Interfaces and developments
Chair: Brian Weitzner
- 4:50-5:10pm Oleg Sobolev, TBD, Python/C++ interface in Phenix suite
- 5:10-5:30pm Markus Heinomen, Aalto University, Protein search by machine learning
4:50-5:30pm Session 7B (Woodpecker)
Broad Topic: Rosetta and evolution
Chair: Jeremy Mills
- 4:50-5:10pm Christoffer Norn, Lund, Rosetta Simulates Evolution
- 5:10-5:30pm Jordan Willis, TSRI, Rosetta Supplemented Mammalian Library Design
5:30-7:30pm Dinner (Kingfisher)
7:30-8:15pm Keynote Session 2 (Chapel & video streaming to Woodpecker)
Chair: TBD
- Ian Wilson, TSRI, Structure-based design of universal influenza vaccines and therapies
8:30pm Poster Session 2 (Quail and Tadpole)
9:30pm Open Bar and Alternative activities
9:30 pm Pub Quiz Style Trivia Night (Flicker)
10:00 pm Annual Carcassonne Tournament, Round 2
Day 3: Thursday, August 10th
7:30-9:00am Breakfast (Kingfisher & Icicle Village)
9:00-10:20am Session 8A (Chapel)
Broad Topic: Drug Design
Chair: Xavier Ambroggio
- 9:00-9:20am Rocco Moretti , Vanderbilt, RosettaDrugDesign: Automated design of small molecules in Rosetta
- 9:20-9:40am Lin Jiang, UCLA, Rosetta Computer Aided Drug Discovery of Alzheimer's Disease
- 9:40-10:00am Melvin Young, BMC, Designed orthogonal membrane receptor-effector switches signal with high pathway selectivity
- 10:00-10:20am Vikram Mulligan, UW, Design of cyclic peptides made from diverse non-canonical building blocks, with novel folds and functions
9:00-10:20am Session 8B (Woodpecker)
Broad Topic: Membrane proteins and beyond
Chair: Julia Koehler Leman
- 9:00-9:20am Patrick Barth, BCM, Stabilizing membrane proteins by design: proofs of concept and challenging targets
- 9:20-9:40am Amanda Duran, Vanderbilt, Improvements in Thermostability Predictions and Evaluation of Design of Membrane Proteins in Rosetta
- 9:40-10:00am Assaf Elazar, Weizmann, Deciphering membrane protein energetics using deep sequencing; Towards robust design and structure prediction of membrane proteins
- 10:00-10:20am Jason Lai, BCM, Enhancing structure prediction and design of soluble and membrane proteins with explicit solvent-protein interactions
10:25-10:40am Coffee Break (Salmon Gallery)
10:40am-12:00pm Topic-Focused Break-Out Discussions
- Rosetta is a Cheeseburger - Intro to Rosetta (Woodpecker)
- Speaker: Steven Lewis, Cyrus
- Funding opportunities at the NSF (Green Room Chapel)
- Moderator: Jenifer Weller
- Speaker: Jenifer Weller, NSF
- Non-canonicals and Glycans in Rosetta (Grotto Pub)
- Moderator: Jeff Gray
- Chalk talk: Jared Adolf-Bryfogle, TSRI, Modeling Carbohydrates: From roots to foliage
- Chalk talk: Jacob Miner, LANL, New approaches for describing peptoid structures with Rosetta
- Enzyme Design (Flicker)
- Moderator: Sagar Khare
- Chalk talk: Sagar Khare, Rutgers, Rosetta-Guided Protein Stapling for Enzyme stabilization
- Chalk talk: Brahm Yachnin, Rutgers, Computational Design of Non-Immunogenic, Activatable, Next-Generation DEPT Chemotherapy Enzymes
- Chalk talk: Rene de Jong, DSM, Enzyme substrate specificity redesign using coupled_moves in Rosetta
- Protein Docking (Nuthatch)
- Moderator: Sarel Fleishman
- Chalk talk: Santrupti Nerl, UCSC, Expanding the HLA repertoire for specific peptides
- Small Molecule/Drug Design with Rosetta (Salmon Gallery Terrace)
- Moderator: Rocco Moretti
- Chalk talk: Nir London, HU, Bond, covalent Bond
- Design of repeat proteins (Kingfisher Terrace)
- Moderator: Fabio Parmeggiani
- Chalk talk: Phil Bradley, FHCRC, Design of tandem repeat proteins
- Challenges on the design of protein therapeutics (Quail Porch)
- Moderator: Dan Kulp
- Chalk talk: Stephan Kudlacec, UNC, Designing Zika and Dengue Envelope Protein Dimer Vaccine
- Chalk talk: Hua Bai, UW, Modulating immune tolerance by utilizing computational protein design
12:00pm-2:00pm Lunch (Kingfisher)
2:00-3:00pm Session 10A (Chapel)
Broad Topic: Enzyme Design II
Chair: TBD
- 2:00-2:20pm Kristin Blacklock, Rutgers, Computational design of a photosensitized yeast cytosine deaminase for directed enzyme-prodrug therapy
- 2:20-2:40pm Gideon Lapidoth, Weizmann, Using evolutionary principles to design novel enzymes
- 2:40-3:00pm Alex Dylan Carlyn, UCDavis, Data-driven enzyme engineering
2:00-3:00pm Session 10B (Woodpecker)
Broad Topic: PPI Design
Chair: Eva-Maria Strauch
- 2:00-2:20pm Ora Schueler-Furman, HU, Challenges and successes in the design of inhibitory peptides and peptidomimetics
- 2:20-2:40pm Ravit Netzer, Weizmann, Computational design of a large network of specific and multispecific protein-protein interactions
- 2:40-3:00pm Jack Maguire, UNC, Monte Carlo methods for designing hydrogen bond networks
3:00-4:00pm REU/Intern Debriefing Session (Woodpecker)
Chair: Jeff Gray
3:00-5:30pm Poster Session 3 (Quail and Tadpole)
Woodpecker
3:00-3:30pm Coffee Break (Salmon Gallery)
5:00pm Annual Swim Across Icicle Creek
5:30-7:30pm Dinner (Kingfisher)
7:20-7:30pm Presentation of Rosetta Service and Poster Awards
7:20-8:15pm Keynote Session 3 (Chapel & video streaming to Woodpecker)
Chair: TBD
- Shoshana Wodak, VIB, Modeling Protein-protein interactions: then and now
8:15-8:30pm Closing Session (Chapel)
8:30pm PI Meeting (Fire Pit by the Creek)
9:30pm Open Bar and Alternative Activities
9:00 pm Open Board Game Night (Flicker)
10:00 pm Annual Carcassonne Tournament, Round 3
Day 4: Friday, August 11th
7:30-9:00am Breakfast (Kingfisher & Icicle Village)
9:00am Bag lunch, checkout, and van/hike departures