Agenda*
Tuesday - August 3rd (afternoon only)
12:00-1PM Lunch
1PM Session 0: Introductions - Chairs: Charlie EM Strauss and Richard Bonneau
3:30PM Session 1: Topic TBA - Chair: Bill Schief
Capturing and Publishing Protocols, a RosettaCon special issue?
Rich Bonneau
New Developments in Rosetta Ligand - 20 min
Jens Meiler - Meiler Lab
An ansatz for breaking the conformational sampling bottleneck in high-resolution RNA and protein folding - 20 min
Rhiju Das - Das Lab
Peptoid Structure and Design - 20 min
Glenn Butterfoss, Doug Renfrew - Bonneau Lab
Invited Talk - 20 min
Jane Richardson, Duke
Break - 10 minutes
Beverage & Snack BreaksBreaks with complimentary beverages and snacks will be interspersed with the talks. |
Beverages
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Snacks
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Workshop 1: Parallel sessions - Chair: TBA
Parallel session 1: (Main auditorium)
IRON CHEF ROSETTA 1: Tutorial on scripting the XML interface to mini - 20 min + questions
Sarel Fleishman - Baker Lab
Parallel session 2: (Campfire pit)
PI Meeting 1: BTRR (1 hour)
6-7PM Dinner
7:20PM After Dinner Keynote Lecture
Colonel David Wombat Baker presents his Wild West Rodeo and singing postdoc review.
Children and persons of weak constitution barred at the door. - 30 min
7:50-9:50PM Poster Session 1
9-11PM Drinks
Sponsored by:
Wednesday - August 4th
7:30-8:30AM Breakfast
9AM Session 2: Movement - Chair: Rhiju Das
Antibody binding to anthrax edema factor determined by RosettaDock using flexible loop modeling - 20 min
Michael A. Dolan, Ph.D. - NIH/NIAID
Flexibility Prediction: Preserving Detailed Balance in Side Chain and Backbone Movers - 20 min
Colin A. Smith - Kortemme Lab
Mapping the 'Farnesylome' - Structure-based Prediction of Farnesyl Transferase Targets - 20 min
Nir London - Schueler-Furman Lab
Transplantation of a complex binding site using computational design and in vitro evolution - 20 min
Correia B., Azoitei M. L., Ban Y. A., Kalyuzhniy O., Schroeter A., Baker D., Schief W. R. University
10:25AM Break
10:40AM Session 3: - Chair: Tanja Kortemme
Invited Talk - 30 min
Adam Godzik, The Burnham Institute, La Jolla
Computational design of a new protein-protein interface between Gil and a redesigned RGS14 GoLoco - 15 min
Deanne Sammond - Kuhlman Lab
Computational de novo design of "ideal" protein structures - 20 min
Nobuyasu Koga, Rie Koga - Baker Lab
*note: not willing to share slides, please take notes!
The new fragment picker - 15 min
Dominik Gront - Baker Lab
12:00-1PM Lunch
1:30PM Session 4: Structure Determination and Prediction - Chair: Phil Bradley
A hydrogen-bond centric view of protein solvation - 20 min
John Karanicolas and R.W. Smith - Karanicolas Lab
Tuning and Validating Rosetta: H-Bonds with OH donors - 20 min
Matthew O'Meara - Kuhlman Lab
Rosetta refinement in medium resolution density maps reaches atomic resolution for proteins of up to 350 residues - 20 min
Steffen Lindert - Meiler Lab
Laying-out and Lacing-up Ligand Locations Linked into Rosetta and expressed in the Laboratory - 20 min
Loren L. Looger - Janelia Farms
2:50PM Break
The Rosetta Design Group would like to thank the Participants, the Rosetta Commons Community, the University of Washington, and the Sleeping Lady Mountain Retreat for making this event possible. |
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3:10PM Session 5: Design - Chair: Jim Havranek
Designing Metal Templated de novo Protein Complexes - 20 min
Xavier I. Ambroggio - Rosetta Design Group
Prediction of temperature sensitive mutations - 20 min
Chris Poultney - Shasha, Bonneau Labs
RosettaEPR: An Integrated Tool for Protein Structure Determination from Sparse EPR Data - 20 min
Stephanie Hirst - Meiler Lab
IRON CHEF ROSETTA 2: Write a practical Mini Protocol, live demo with rotating knives - 25 min
Rhiju Das - Das Lab
4:30-6PM Flexible Time
A few words about RTmin - 10 min
Andrew Leaver-Fay - Kuhlman Lab
Workshop:
IRON CHEF ROSETTA 3: Tutorial on PyRosetta for research, dancing with wolves in 3D.
Brian Weitzner, Andrew Leaver-Fay, Dan Kulp, Sergey Lyskov
6-7PM Dinner
7:20-8:10PM Session 6: Interfaces to Rosetta - Chair: John Karanicolas
Standalone Foldit: A New and Powerful Interface to Rosetta - 20 min
Matthew Smith - Baker Lab
Pymol-PyRosetta Integration - 20 min
Brian Weitzner and Evan Baugh - Gray Lab
7:50-9:50PM Poster Session 2
9-11PM Drinks
Thursday - August 5th
7:30-8:30AM Breakfast
9AM Session 7: Mini talks (and a science talk) - Chair: Jens Meiler
Can Self-Inhibitory Peptides be Derived from the Interfaces of Globular Protein-Protein Interactions? - 20 min
Ora Schueler-Furman - Schueler-Furman Lab
Non-natural Peptide Inhibitor Design of Amyloid Fibrils - 20 min
Lin Jiang - Eisenberg Lab
Binding predictions for peptide recognition modules - 20 min
Joseph Crivelli- Meiler Lab
De novo design of nanomolar affinity protein binders of the conserved region on influenza hemaglutinin - 20 min
Sarel Fleishman - Baker Lab
11AM Round Table about current challenges - Chairs: Charlie EM Strauss and Richard Bonneau
Where's the Beef?
12-1PM Lunch
1:30PM Session 9: Mixed nuts - Chair: Ora Schueler-Furman
Introduction to JD2 - 15 min
Steven Lewis - Kuhlman Lab
Update on the Testing Infrastructure in Rosetta - 15 min
Sergey Lyskov - Gray Lab
Incorporating the Rosetta Force Field into GPUs with Open MM Molecular Mechanics - 20 min
Peter Eastman - Pande Lab
Appplication of Rosetta to GPCR Homology Models - 15 min
Elizabeth Dong, Karen Gregory, Jeff Conn, Jens Meiler - Meiler Lab
Roll out the beta barrel - 15 min
Will Proffitt - Meiler Lab
2:50PM Break
3:10PM Session 10: Binding and Specificity - Chair: Rich Bonneau
He's dead, Jim - 20 min
Jim Havranek - Havranek Lab
A Multistate Design Protocol for your Multistate Design Problem - 20 min
Andrew Leaver-Fay - Kuhlman Lab
EteRNA - a multiplayer RNA videogame with high throughput experimental validation - 15 min
Jeehyung Lee, Wippat Kladwang, Stephanie Federwisch, Ming yao, Christopher VanLan, Jonathan Ciscon, Noah Fishel, Rhiju Das, Adrien Treuille
How to Teach a course Using PyRosetta - 15 min
Jeff Gray - Gray Lab
4:30-6PM Workshops
Workshop 2:
Mini and me, what needs fixing? Godot.wait().self.observer(get_factory(Godot)) - 25 min
Led by Andrew Leaver-Fay and Jeff Gray
6-7PM Dinner
7:30-9PM Summary and Hike Organization
9-11PM Drinks
9-10PM PIs Meeting
About the Rosetta Design Group
The Rosetta Design Group LLC was established in 2007 to bridge the gap between the Rosetta Commons academic community and the pharmaceutical industry.
RDG provides services ranging from assistance to 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. Select examples of areas of R&D: |
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| Homology modeling | Antibody modeling and epitope mapping |
| Protein design and stabilization | Protein-protein interface design and analysis |
| Protein-peptide interactions, design and analysis | |
Typically, 2-3 days of tailored instruction and hands-on tutorials. Training can be broadcasted live to multiple sites. |
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Networking and the cutting edge of Rosetta development |
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Rosetta support resources, events, the Macromolecular Modeling Blog™, and more. |
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Industry Participants
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| Andrew Ban Arzeda |
Louis Clark Codexis |
Jacob Corn Genentech |
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| Michael Dolan NIAID |
Andrei Golosov Merck |
Katarina Midelfort Pfizer |
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| Cecile Morales ProteinAI |
Eliud Oloo Sanofi Pasteur |
Arvind Sivasubramanian Adimab |
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| Vanita Sood EMD Serono |
Jain Tush Adimab |
Alexandre Zanghellini Arzeda |
Rosetta Commons Participants
- Rosetta Design Group
- Xavier Ambroggio
- Monica Berrondo
- University of Washington
- David Baker
- Florian Richter
- Summer Thyme
- Kui Chan
- Eva-Maria Strauch
- Firas Khatib
- Sinisa Bjelic
- TJ Brunette
- Matt Smith
- Erik Procko
- Yuan Liu
- Vladimir Yarov-Yarovoy
- Sarel Fleishman
- Justin Siegel
- Rocco Moretti
- Fabio Parmeggiani
- Jeremy Mills
- James Moody
- Tim Whitehead
- Dominik Gront
- Austin Day
- Yifan Song
- Oliver Lange
- Frank DiMaio
- Nobuyasu Koga
- Rie Koga
- Sridharan Rajagopalan
- James Thompson
- Robert Vernon
- Lucas Nivon
- Sagar Khare
- Ray Wang
- David Kim
- Liz Kellogg
- Sandrine Boissel
- Alexej Grjasnow
- Gustav Oberdorfer
- Nikolas Sgourakis
- Burnham Institute & UCSD
- Adam Godzik
- New York University
- Richard Bonneau
- P. Douglas Renfrew
- Dennis Shasha
- Chris Poultney
- Glenn Butterfoss
- Timothy Craven
- Noah Youngs
- Ken Ho
- FHCRC, Seattle
- Phil Bradley
- Shen Li
- Chen Yanover
- Fox Chase Cancer Center
- Roland Dunbrack
- The Hebrew University
- Ora Furman
- Nir London
- Lior Zimmerman
- Eran Kuchuk
- Chaim Dryzun
- ETH Zurich
- Lars Malmstroem
- Abdullah Kahraman
- Peter Kunszt
- Duke University
- Jane Richardson
- University of Colorado
- Hubert Yin (not attending)
- Deanne Sammond
- Betty Eskow
- UCLA
- David Eisenberg (not attending)
- Lin Jiang
- Luki Goldschmidt
- Washington University
- Jim Havranek
- Chi Zhang
- Ben Borgo
- University of California
- San Fransisco
- Tanja Kortemme
- Noah Ollikainen
- Colin Smith
- Dan Mandell
- Cristina Melero
- University of North Carolina
- Chapel Hill
- Brian Kuhlman
- Andrew Leaver-Fay
- Steven Lewis
- Oana Lungu
- Ron Jacak
- Matthew O'Meara
- Ben Stranges
- Hayretin Yumerefendi
- The Johns Hopkins University
- Jeff Gray
- Sergey Lyskov
- Brian Weitzner
- Krishna Praneet Kilambi
- Robin Augustine Thottungal
- Moon Young "Liza" Lee
- Jianqing Xu
- Evan Baugh
- Joshua Austin
- Los Alamos National Lab
- Charlie Strauss
- Dan Kulp
- Ramesh Jha
- Defense Threat Reduction Agency
- Revel Williams
- University of Pennsylvania
- William Degrado (not attending)
- Jenny Hu
- Lund University
- Ingemar Andre
- Sebastian Ramisch
- Vanderbilt University
- Jens Meiler
- Stephanie Hirtt
- Sam DeLuca
- Gordon Lemmon
- Elizabeth Dong
- Steffen Lindert
- Joe Crivelli
- Will Proffitt
- Brittany Allison
- Jordon Willis
- Andrew Morin
- David Nannemann
- Dietmar Birzer
- Hermann Zellner
- University of Washington
- Bill Schief
- Sergey Menis
- Oleksandr Kalyuzhniy
- Possu Huang
- Andreia Serra
- Chris Carrico
- Joe Jardine
- Justin Porter
- Stanford
- Rhiju Das
- University of Kansas
- John Karanicolas
- Ragul Gowthaman
- David Johnson
- Whitney Smith
- Rutgers University
- Alex Morozov
- Janelia Farms, HHMI
- Loren Looger
- Stanford University
- Vijay Pande (not attending)
- Peter Eastman
- University of Washington
- UW Tech Transfer Office
- Angela Loihl