Rosetta Design Group LLC

Day 1: Wed, July 30th

8:45 AM Van departures from UW dorms
9:15 AM Van departures from UW South Center
12-1:30 PM Lunch at Kingfisher
1:30-3:10 PM Session 1 (plenary)*: Grand Challenges in Rosetta. Chair: Sagar Khare (Rutgers U)

1:30-1:35 Introduction and Welcome
1:35-1:40 RosettaCON Code of Conduct (Brian Weitzner)
1:40-2:05 Phil Bradley (FHCRC) & Frank DiMaio (UW): Waters in Rosetta
2:05-2:25 Scott Boyken (UW) - Design of Hydrogen Bond Networks in Rosetta
2:25-2:45 Andrea Bazzoli (KU) � SHO model for polar solvation
2:45-3:10 Rhiju Das (Stanford) - Five reasons to get RNP's into Rosetta
*Seating will be available in both Chapel and Woodpecker for plenary sessions. Proceedings (including slides) will be broadcast from Chapel to Woodpecker

3:10-3:30 PM Coffee break (coffee/snacks @both Woodpecker and Chapel)
3:30-5:15 PM Small Groups Session 1

Various places (flip-chart research talks ~10-15 mins) - group-meeting style.

Go to your assigned group: Small Group Assignments
Playbarn: Industry Participant Orientation (flip-chart available, 5-7 min introductions)

5:15-5:45PM Check into rooms, Setup Posters

5:45-7PM Dinner at Kingfisher (Meeting for students/PIs attending the Grace Hopper Conference)
7:15-8:15PM Keynote Speaker: David Baker (U Washington). TBA
8:15PM Poster session I, Beer, and Company

Day 2: Thursday, July 31st

7:30-9AM Breakfast at Kingfisher

Mentoring table:

9-10:40 AM Topic-focussed break-out discussions and Rosetta Programming Tutorial

Discussion groups around specific scientific topics. See: Breakout Discussion Topics List
Chapel: Steven Lewis tutorial ("Beginner's tutorial for programming in Rosetta a.k.a Rosetta is a Cheeseburger")

10:40-11:00 AM Coffee break
11:00 -12 PM Session 2 (parallel session)

Chapel: Small-molecule Inhibitor Design. Chair: Justin Siegel (UC Davis)

11:00-11:20 AM Vladimir Yarov-Yarovoy (UC Davis) - Towards rational design of novel analgesics
11:20-11:40 AM Abba Leffler (NYU) - Engineering Selectivity and Potency into Peptide Natural Products with Multistate and Non-Canonicals (and Docking and Loop Modeling?)
11:40-12:00 PM Nir London (UCSF) - Covalent Docking of Large Libraries for the Discovery of Chemical Probes

Woodpecker: RNA and RNA-protein interactions. Chair: Jim Havranek (Wash U)

11:00-11:20 AM Jane Richardson - ERRASing Local Errors in RNA Crystal Structures
11:20-11:40 AM Ragul Gowthaman (KU) - Identifying inhibitors of protein-RNA interactions by structural mimicry
11:40-12:00 PM Clarence Cheng (Stanford) - Multiplexed �OH Cleavage Analyzed by Sequencing: RNA 3D models from chemically mapped pairwise distance constraints

12:00-1:30 PM Lunch at Kingfisher

Mentoring Table: Women in Rosetta/Science (Mentors: Tanja Kortemme, Ora Schueler-Furman)

1:30-3 PM Small Groups Session 2

Various places (flip-chart talks) - group-meeting style.

Go to your assigned group: Small Group Assignments

3-3:30 PM Coffee Break
3:30-5:30 PM Session 3 (plenary): Design of Novel Protein Structures. Chair: Tim Whitehead (Michigan State U)

3:30 - 4:00 PM Sebastian R�misch (Lund U)- Computational design of shape-optimized Leucine rich repeat proteins
4:00 - 4:30 PM Birte Hocker (Max Planck Inst) - New proteins from smaller fragments
4:30 - 5:00 PM Tim Jacobs (UNC) - Automated assembly of protein substructures for the generation of de novo protein backbones
5:00 - 5:30 PM Gevorg Grigoryan (Dartmouth) - Computational Design of Selective Targeting Peptides

5:45-7PM Dinner at Kingfisher
7:15-8:15PM Keynote Speaker: Andrej Sali (UCSF) - Integrative Structural Biology
8:15PM Poster session II, Beer, and Company

Day 3: Fri, Aug 1st

7:30-9AM Breakfast at Kingfisher

Mentoring table: How to prepare and pursue leadership positions outside academic science (Mentors: Michelle Dohm, Deanne Sammond, Alex Zanghellini, Jiye Shi) [industry attendees, if you are willing to attend and mentor, it will be great and much appreciated]

9-10:40 AM Topic-focussed break-out discussions

Discussion groups around specific scientific topics. (feel free to go to a different group)

See: Breakout Discussion Topics List
Woodpecker: (Steven Combs/Rocco Moretti) �New drug design and docking modules in Rosetta and drug design puzzle sets in FoldIt
Playbarn: (Chair: Xavier Ambroggio, RDG) Rosetta and Industry
- 9:00-9:30 AM Alexandre Zanghellini (Arzeda) - Rosetta in industrial and synthetic biology
- 9:30-10:00 AM Lucas Nivon & Yinfan Song (Cyrus Biotechnology) - Commercializing Rosetta
- 10:00-10:30 AM Roundtable on Improving Rosetta for Industry
- 10:30-10:40 AM Industry Collaborations/Networking/Recruiting Session
Chapel: (Sergey Lyskov) - Rosetta Benchmarking
- Benchmark-2, progress report and future directions. Sergey Lyskov
- Scientific tests for energy function and sampling improvements with protocol captures. Shane O'Connor
- Do we need additional build tests? (Clang+MPI, icc, etc.)
- Separate status for broken integration tests?
- Metrics for Scientific Tests (Discussion).
- General discussion on Rosetta Benchmark and Testing.

10:40-11:00 AM Coffee break
11:00 -12 PM Session 4 (parallel session)
Chapel: Protein-protein Interface Design. Chair: Ora Schueler-Furman (Hebrew U.)

11:00-11:20 AM Aaron Chevalier (UW) - High Throughput Design and Testing of 12,472 De Novo Influenza Binders
11:20-11:40 AM Julia Shifman (Hebrew U) � Mapping binding landscapes with computation and experiment
11:40-12:00 PM Ryan Hallet (UNC) - Engineering an improved light-induced dimer for controlling the localization and activity of signalling proteins

Woodpecker: Structure prediction/determination with experimental data. Chair: Liz Kellogg (Berkeley)

11:00-11:20 AM Lars Malmstroem (ETH) - Targeted chemical crosslinking mass spectrometry for rapid experimental validation of protein-protein docking simulations
11:20-11:40 AM Nik Sgourakis (NIH) - Modelling naturally occurring helical bundle-based filaments and assemblies using solid-state NMR and cryoEM data
11:40-12:00 PM Colin Smith (Max Planck Inst) - Identifying Concerted Backbone and Side Chain Motion Using NMR and MD Simulation

12:00-1:30 PM Lunch at Kingfisher

Mentoring table: Developing and implementing Rosetta teaching materials for classes and workshops (Host: Oana Lungu, Mentors: TBA)

1:30 - 1:50 PM Session 5.1 (plenary) State of the Commons

1:30-1:45 PM Jennifer McCullar (UW C4C) - Summary of Rosetta Licensing
1:45-1:50 PM General discussion

1:50 - 3:10 PM Session 5.2 (plenary) Gender and Science, Chair: Jeffrey Gray (Johns Hopkins)

1:50-2:00 PM Jeffrey Gray (Johns Hopkins) - Diversity efforts within the Rosetta Commons

2:00-3:00 PM Karen Fleming (Johns Hopkins) - Achieving Gender Equity: How can women move beyond bias and barriers? GenderEquity-Fleming.pdf
3:00-3:10 PM General Discussion

3-3:30 PM Coffee Break
3:30-4:30 PM Session 6.1 (plenary): Recent Highlights in Rosetta Applications & Development Chair: Firas Khatib (U Mass)

3:30 - 4:00 PM Elizabeth Kellogg (UC Berkeley) - Combining high-resolution Cryo-EM and Rosetta to resolve the stabilizing effect of Taxol on the microtubule lattice
4:00 - 4:30 PM Alex Ford (UW) - Structure structure database in turn and sequence design

4:30-5:30 PM Session 6.2 (plenary): Antibody modeling and design. Chair: Chu Wang (Peking U)

4:30 - 5:00 PM Olga Khersonsky for Gideon Lapidoth (Weizmann Inst.)- AbDesign: A method for computational antibody design guided by natural conformations and sequences
5:00 - 5:30 PM Jens Meiler (Vanderbilt U.) - Antibody/Antigen Complexes: Prediction of Structure and Design of Function

5:45-7PM Dinner at Kingfisher
7:15-7:30PM Hike Organization (Chair: Brian Kuhlman)
7:30-8:00PMDiscussion about PLoS Special Issue format
8-9PM PI Meeting

Day 4: Saturday, Aug 2nd

7:30-9AM Breakfast at Kingfisher
9:00 AM: Bag lunch, checkout, and van/hike departures


	The Rosetta Design Group thanks all Participants, the RosettaCommons Community, the University of Washington, and the Sleeping Lady Mountain Retreat for making this event possible.


Feng Dong Abbvie	Takaaki Fukami Chugai	Greg Lakatos Zymeworks

Alexandre Zanghellini Arzeda	Jiye Shi Xiaofeng Liu UCB	Zara Fulton Antonietta Impagliazzo Crucell

David Nannemann EMD Serono	Jianqing Xu MedImmune	Rene de Jong DSM Biotechnology Center

David Riddle USAF	Ryan Stafford Sutro Biopharma	Govindan Subramanian Zoetis

RosettaCON2014
July 30th - August 2nd 2014, Leavenworth, WA

Day 1: Wed, July 30th

Day 2: Thursday, July 31st

Day 3: Fri, Aug 1st

Day 4: Saturday, Aug 2nd

About the Rosetta Design Group

Industry Participants

Academic Participants

About the Rosetta Design Group The Rosetta Design Group LLC was established in 2007 to bridge the gap between the RosettaCommons academic community and industry.


Contract R&D in modeling and bioinformatics The Rosetta Design Group provides services ranging from assistance for computational scientists in protocol development to fully out-sourced R&D in structural modeing and bioinformatics for computational and experimental groups whose demands exceed their in-house capacities.


Rosetta Design Group Website: http://www.rosettadesigngroup.com ROSETTA resources, events, jobs, the Macromolecular Modeling Blog™, and more.

RosettaCON2014 July 30th - August 2nd 2014, Leavenworth, WA

Day 1: Wed, July 30th

Day 2: Thursday, July 31st

Day 3: Fri, Aug 1st

Day 4: Saturday, Aug 2nd

About the Rosetta Design Group

Industry Participants

Academic Participants

RosettaCON2014
July 30th - August 2nd 2014, Leavenworth, WA