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



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The Rosetta Design Group


Members

Xavier Ambroggio

 
(far left, green shirt)

Nir London

 
(back row, orange jacket)

Glenn Butterfoss

  (center front, blue jacket)
Monica Berrondo  
(not pictured)
   
Scientific and Executive Advisory Board
David Baker, UW  
(2nd from right, blue fleece)
Brian Kuhlman, UNC  
(far right, grey jacket)
Jeffrey Gray, JHU  
(not pictured)
Gabrielle Campbell, AAMC  
(not pictured)



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.

 
     



 

Beverage & Snack Breaks

Breaks with complimentary beverages and snacks will be interspersed with the talks.
  Beverages
  • Regular & Decaf Coffee, Tea, Cider, & Hot Chocolate
  • Assorted Fruit Juices, Soft Drinks and Water
 
Snacks
  • Sliced Fresh Fruit, Vegetables, Crackers, Assorted Cheeses
  • Freshly Baked Cookies and Brownies

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


Friday - August 7th


7:30-9AM Hike Departure!


1:30PM Departure



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.


backbone
  • Contract R&D Modeling & Bioinformatics

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:

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
 
  • On-site Training

Typically, 2-3 days of tailored instruction and hands-on tutorials. Training can be broadcasted live to multiple sites.

 
  • Webinars

Tutorials on select topics for scientists in academic and non-profit settings.

 
  • RosettaCon

Networking and the cutting edge of Rosetta development

 
  • Rosetta Design Group Website: http://www.rosettadesigngroup.com

Rosetta support resources, events, the Macromolecular Modeling Blog™, and more.


moutain

Industry Participants


Name  
Organization
Shaun Lippow  
Aileron
James Apgar  
Agrivida
Justin Caravella  
Biogen IDEC
Louis Clark  
Codexis
Katarina Midelfort  
Pfizer (Groton)
Andrea Rossi  
Pfizer (Rinat)
Andrei Golosov  
Merck
Feng Dong  
Merck
Jonathan H. Davis  
Adnexus
Vanita Sood   EMD Serono
Darrell Hurt   NIH, Lockheed Martin
Kristian Krantz   Novo Nordisk
Sean Hodgins   USAMRICD
James Zhu  
USDA ARS






Rosetta Commons Participants


Rosetta Design Group

New York University

University of California

Vanderbilt University

Xavier Ambroggio

Rich Bonneau

Santa Cruz

Jens Meiler

Chris Poultney

Karplus Lab

Gordon Lemmon

University of Washington

Glenn Butterfoss

Firas Khatib

Stephanie Hirst

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

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

 

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