Agenda
RosettaCon2009
Tuesday - August 4th (afternoon only)
12:00-1PM Lunch
1PM Session 0: Introductions - Chairs: Phil Bradley & Ora Schueler-Furman
3:30PM Session 1: Topic TBA - Chair: Brian Kuhlman
Enzyme design
Justin Siegel - Baker Lab
Design of genetically encoded photoactivatable proteins
Oana Lungu - Kuhlman Lab
Little RNA puzzles can be surprisingly hard
Rhiju Das - Stanford
Building up to Peptoid design, Designing TS mutants, Scaling rosetta to genome annotation
Rich Bonneau - NYU
6-7PM Dinner
7:20PM After Dinner Keynote Lecture - David Baker
7:50-9:50PM Poster Session I
9-11PM Drinks
Wednesday - August 5th
7:30-8:30AM Breakfast
9AM Session 2: Structure prediction - Chair: Rhiju Das
Flexible peptide docking
Barak Raveh - Schueler-Furman Lab
Kinematic Closure with Constraints
Vageli Coutsias - University of New Mexico
Kinematic closure for interface remodeling and design
Dan Mandell - Kortemme Lab
Structure prediction of Metal Binding Proteins
Chu Wang - Cravatt Lab
The Rosetta Design Group
Members |
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Xavier Ambroggio |
(far left, green shirt) |
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Nir London |
(back row, orange jacket) |
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Glenn Butterfoss |
(center front, blue jacket) | |
| Monica Berrondo | (not pictured) |
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Scientific and Executive Advisory Board |
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| David Baker, UW | (2nd from right, blue fleece) |
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| Brian Kuhlman, UNC | (far right, grey jacket) |
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| Jeffrey Gray, JHU | (not pictured) |
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| Gabrielle Campbell, AAMC | (not pictured) |
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10:40AM Session 3: Binding and Specificity Prediction - Chair: Tanja Kortemme
Specificity prediction
Chen Yanover & Chris King - Bradley Lab
Specificity Prediction and Design of Phosphoswitches
Colin Smith - Kortemme Lab
ΔΔG prediction
Liz Kellogg - Baker Lab
Improving the Rosetta energy function
Yifan Song - Baker Lab
12:00-1PM Lunch
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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Beverage & Snack BreaksBreaks with complimentary beverages and snacks will be interspersed with the talks. |
Beverages
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Snacks
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1:30PM Session 4: Design - Chair: John Karanicolas
Remodel
Possu Huang - Schief Lab
Design of proteins to interact with biominerals
Dave Masica - Gray Lab
Surface Design
Sam DeLuca - Meiler Lab
Simultaneous optimization of solubility and stability in protein design simulations
Ron Jacak - Kuhlman Lab
3:10PM Session 5: Ligand docking - Chair: Jim Havranek
Fitting into electron density
Frank DiMaio - Baker Lab
Multi ligand docking with ligand rotamers
Gordon Lemmon - Meiler Lab
Small Molecule Docking to Homology Models
Kristian Kaufmann - Meiler Lab
Rosetta design of protein ligand interfaces
Andrew Morin - Meiler Lab
Modeling antibody-antigen complexes to improve biotherapeutics
Andrea Rossi - Rinat-Pfizer
6-7PM Dinner
7:20PM Round Table about current challenges - Chairs: Phil Bradley & Ora Furman
7:50-9:50PM Session 6: Interfaces to Rosetta- Chair: Xavier Ambroggio
Using Mini/Rosetta3.x as an API (with E2/E3 interactions as an example)
Steven Lewis - Kuhlman Lab
PyRosetta for the broader community
Sid Chaudhury, Sergey Lyskov, & Jeff Gray - JHU
Enzyme design in Mini
Florian Richter - Baker Lab
RosettaParser
Justin Ashworth - Baker Lab,
7:50-9:50PM Poster Session II
9-11PM Drinks
Thursday - August 6th
7:30-8:30AM Breakfast
9AM Session 7: Mini talks - Chair: Jens Meiler
Remaining mini hurdles
Andrew Leaver-Fay - Kuhlman Lab
Testing infrastructure in Rosetta
Sergey Lyskov - Gray Lab
RosettaScripts
Sarel Fleishman - Baker Lab
Brokers
Oliver Lange- Baker Lab
11AM Session 7: Mini free time - Chair: Jeff Gray
12-1PM Lunch
1:30PM Session 9: Rosetta Science - Chair: Bill Schief
Statistical mechanics of nucleosome positioning
Alex Morozov - Rutgers University
Endonuclease design
Umut Ulge - Baker Lab
Statistical energy functions in Rosetta
Roland Dunbrack - Fox Chase Cancer Center
On the origin of symmetry
Charlie Strauss - Los Alamos National Laboratory
3:10PM Session 10: More Interesting Science Chats - Chair: Rich Bonneau
The phone cord effect in the formation of helical crossovers and knotted proteins
Chris Bystroff - Rensselaer Polytechnic Institute
Engineering proteins for the brain
Loren Looger - HHMI Janelia Farm
Stapled peptides and other applications in protein engineering
Shaun Lippow - Aileron
FoldIt
Jeehyung Lee - Treuille Lab
Fast Relax, Homology Modelling and Energy Landscape Exploration
Mike Tyka - Baker Lab
6-7PM Dinner
7:30-9PM Summary and Hike Organization
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. A sampling of RDG activities are listed below.
RDG has provided and continues to provide services ranging from assistance to computational scientists in protocol development to fully out-sourced modeling R&D 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 & sequence alignments | Antibody modeling and epitope mapping |
| Protein design and stabilization | Protein-protein interface design and analysis |
| Protein-small molecule interaction designs 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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Tutorials on select topics for scientists in academic and non-profit settings. |
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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
| Name | Organization |
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| Shaun Lippow | Aileron |
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| James Apgar | Agrivida |
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| Justin Caravella | Biogen IDEC |
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| Louis Clark | Codexis |
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| Katarina Midelfort | Pfizer (Groton) |
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| Andrea Rossi | Pfizer (Rinat) |
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| Andrei Golosov | Merck |
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| Feng Dong | Merck |
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| Jonathan H. Davis | Adnexus |
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| Vanita Sood | EMD Serono | |
| Darrell Hurt | NIH, Lockheed Martin | |
| Kristian Krantz | Novo Nordisk | |
| Sean Hodgins | USAMRICD | |
| James Zhu | USDA ARS |
Rosetta Commons Participants
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Rosetta Design Group |
New York University |
University of California |
Vanderbilt University |
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Xavier Ambroggio |
Rich Bonneau |
Santa Cruz |
Jens Meiler |
| Chris Poultney |
Karplus Lab |
Gordon Lemmon | |
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University of Washington |
Glenn Butterfoss |
Firas Khatib |
Stephanie Hirst |
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David Baker |
Dennis Shasha | Alexej Grjasnow | |
| Florian Richter | Kevin Drew |
University of California |
Sam DeLuca |
| Jacob Corn |
San Francisco |
Joe Crivelli | |
| Eva-Maria Strauch | FHCRC, Seattle |
Tanja Kortemme |
Steffen Lindert |
| Firas Khatib | Phil Bradley |
Colin Smith | Steven Combs |
| Vladimir Yarov-Yarovoy | Chen Yanover |
Dan Mandell | Jonathan Sheehan |
| Will Sheffler | Shen Li | Sen Liu | Eric S. Dawson |
| James Thompson | Chris King | Vageli Coutsias | Keith Henry |
| Andrew Leaver-Fay | Florian Lauck | Andrew Morin | |
| Sarel Fleishman | Fox Chase Cancer Center |
Noah Ollikainen | Jordan Willis |
| Matthew Smith | Roland Dunbrack |
Kristian Kaufmann | |
| Yifan Song | University of North Carolina |
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| Ling Wang | Rensselaer Polytechnic | Chapel Hill |
University of Washington |
| Ingemar Andre | Institute | Brian Kuhlman |
Bill Schief |
| Sinisa Bjelic | Chris Bystroff | Steven Lewis | Sergey Menis |
| Robert Vernon | Yao-ming Huang | Oana Lungu | Mihai Azoitei |
| Jennifer Bui | Patrick Buck | Ron Jacak | Bruno Correia |
| Lucas Nivon | Matthew O'Meara | Possu Huang | |
| Fabio Parmeggiani | The Hebrew University |
Doug Renfrew | Andrew Ban |
| Alexandre Zanghellini | Furman Lab |
Ben Stranges | Chris Carrico |
| Liz Kellogg | Nir London |
Jack Snoeyink | Andreia Serra |
| Nobuyasu Koga | Barak Raveh |
Bryan Der | |
| Rie Koga | Assaf Faragy | Stanford | |
| Patrick Barth | Johns Hopkins University |
Rhiju Das | |
| Summer Thyme | ETH Zürich | Jeff Gray |
Parin Sripakdeevong |
| Justin Siegel | Lars Malmstroem | Aroop Sircar | Kyle Beauchamp |
| Kui Chan | Moon Young (Liza) Lee | ||
| Austin Day | University of Washington |
Monica Berrondo | University of California |
| Justin Ashworth | UW TechTransfer |
Nathaniel Tippens | Los Angeles |
| Frank DiMaio | Alan Yen |
Krishna Praneeth Kilambi | Eisenberg/Yeates |
| Seth Cooper | Kayode Sanni | Luki Goldschmidt | |
Los Alamos National Lab |
David Masica | Neil King | |
| Washington University | Charlie Strauss |
Sergey Lyskov | |
| Jim Havranek | Dan Kulp | Sid Chaudhury | University of Kansas |
| Chi Zhang |
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John Karanicolas | |
| Rutgers University | Robotics & Biology Lab | Chet Egan | |
| Carnegie Mellon | Alex Morozov | TJ Brunette | David Johnson |
| University | Whitney Smith | ||
| Adrien Treuille | Sandia National Lab | Scripps Research Institute | |
| Jeehyung Lee | Arkin | Cravatt | |
| Greg Friedland | Chu Wang |