Sunday, July 29th, Day 1
(no check-in before 5 pm)
12noon Lunch.
1:15PM Session 0: 30 minute discussion of Con logistics. No lab intros! Chapel.
1:30PM Session 1: Plenary session, chair John Karanicolas. Chapel
- Sergey Lyskov (Gray) and Rhiju Das (Das): RosettaServer: RNA as guinea pig
- Andrew Leaver-Fay (Kuhlman): An Empirical Reparameterization of Rosetta's Hydrogen Bond Potential
- James Fraser (Fraser): Some like it hot - conformational motion from room temp crystallography.
Break 15 min. 3:00-3:15
Beverage & Snack BreaksBreaks with complimentary beverages and snacks will be interspersed with the talks. |
Beverages
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Snacks
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3:15PM Session 2: Plenary session, chair Rich Bonneau. Chapel
- Gordon Lemmon (Meiler): Refactoring Rosetta for chemistry
- Ragul Gowthaman (Karanicolas): raycasting for virual screening
- Doug Renfrew (Bonneau): peptoids, macrocycles, etc.
5-6PM Check-in. Set up Poster Session I (last name A-M) in Quail and Tadpole.
5:30-7PM Dinner
7:20PM After Dinner Keynote Lecture, David. Chapel.
7:45-9:45 Poster Session I (last name A-M) Quail and Tadpole. With drinks and snacks.
9:45 More drinks and snacks! Kingfisher Terrace.
Monday, July 30th, Day 2
7:30-8:30 Breakfast . Take down Poster Session I. Put up Poster Session II (last name N-Z)
9:00 AM Session 3: Plenary session, chair Jens Meiler. Chapel
- Amy Keating (Keating): Measuring and modeling protein-peptide interaction specificity
- Evan Baugh (Bonneau lab): ab initio + co-evolution cst’s
- Rhiju Das (Das): EteRNA
- Bill Schief (Schief): TBA -Vaccine related stuff
Break 15 min. 10:30-10:45.
10:45 AM Split session A, chair Ora Furman. Chapel.
- Phil Bradley (Bradley): MR from structure prediction to solve TAL-DNA complex
- Amelie Stein (Kortemme): high-res sampling of conformational heterogeneity in prediction & design
- Yifan Song (Baker): advances in comparative modeling
- André C. Stiel (Höcker): Computational design of novel fluorescent proteins - the looooong way towards the light
10:45 AM Split session B, chair Bill Schief. Woodpecker.
- Abdullah Kahraman (Malmstroem): Modeling Proteins and their interactions in the PP2A network using cross-link data
- Sam DeLuca (Meiler): RosettaQSAR - protein-ligand docking guided by pharmacophore maps
- Florian Richter (Baker): atomic-level design of a esterase active site.
- Parin Sripakdeevong (Das lab): RNA modeling with NMR
12:00-1:30PM Lunch
1:30-2:30PM Grand Challenges. 3-4 mini overview talks. Chapel.
2:30-3:30PM Grand Challenges breakout
3.30-4.00PM Break. Snacks available outside Chapel theater.
4.00-5.00PM Grand Challenges breakout continued. Take down Poster Session I. Put up Poster Session II (last name N-Z).
5.00-6.00PM Grand Challenges presentation of result. Chapel.
6:00-7:00PM Dinner
7:10PM Session 4: Plenary Session, chair Jeff Gray. Chapel
- Nobu and Rie Koga (Baker): principles for designing ideal protein structures
- Todd Yeates (Yeates): Principles for designing symmetric protein assemblies
8:00-9:45PM Poster Session II (last name N-Z). Quail and Tadpole. With drinks and snacks.
9:45 More drinks and snacks! Kingfisher Terrace.
Tuesday, July 31, Day 3
7:30-8:30 Breakfast
9:00AM Split session A, chair Dominik Gront. Chapel
- Matt O’Meara (Kuhlman): Energy function analysis
- Kevin Drew (Bonneau): Protein-protein interaction inhibitors using noncanonical backbones
- Jeremy Mills (Baker): Design of functional sites with unnatural amino acids
- Jordan Willis (Meiler): Antibody design
9:00AM Split session B, chair Sagar Khare. Woodpecker
- Christie Tinberg (Baker): De novo design of ligand binding
- Ora Schueler-Furman (Furman): full peptide-protein modeling
- Steven Combs (Meiler): knowledge-based potentials for partial covalent interactions
Break 15 min. 10:20-10:35.
10:35AM Split session A, chair Jim Havranek. Chapel
- Daniel Hoersch (Kortemme): Engineering a molecular machine
- Shai Cheng and Yen Kal Ng (Ng): Calibur clustering of decoys
- Sergey (Gray): SVN user statistics
10:35 AM Split session B, chair Charlie Strauss. Woodpecker
- Chris King (Baker): designing out immunogenicity
- Frank DiMaio (Baker): crystallographic refinement in Rosetta
- Jianqing Xu (Gray): RosettaAntibody
12:00-1:30 Lunch
1:15PM Industry participants photo, meeting, and brief Rosetta in industry discussion
1:30PM Picture (near dining hall). PLoS author discussion (Chapel). Free time.
3:05PM Tutorial festival. Meet at Chapel to organize before splitting out.
6:00-7:00PM Dinner
6:20PM Discussion of Rosetta in industry over dinner
Meet inside the dining hall. Look for Xavier, industry participants, or the Rosetta Design Group sign on the table.
7:30-9:00PM Hike and Ride Organization, Chapel.
9:00-10:00PM PI Meeting, Fireside.
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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August 1, Day 4
7:30-9:00AM Hike departures.
About the Rosetta Design GroupThe Rosetta Design Group LLC was established in 2007 to bridge the gap between the Rosetta Commons academic community and the pharmaceutical industry. |
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| 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. |
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| Rosetta Design Group Website: http://www.rosettadesigngroup.com Rosetta support resources, events, the Macromolecular Modeling Blog™, and more. |
Industry Participants
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| Jiye Shi UCB |
Jesper Madsen Novo Nordisk |
Xavier Ambroggio Rosetta Design Group |
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| Andrew Ban Arzeda |
Ye Che James Apgar Joel Bard Pfizer |
Jacob Corn Christian Cunningham Genentech |
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| Vanita Sood EMD Serono |
Lei Jia |
Rene de Jong DSM Biotechnology Center |
Academic Participants
- Rosetta Commons
- Baker Lab
University of Washington - David Baker
- Jacob Bale
- TJ Brunette
- Firas Khatib
- Neil King
- Christopher Miles
- Florian Richter
- Yifan Song
- Nobuyasu Koga
- David Kim
- Jennifer Bui
- Eva-Maria Strauch
- Rocco Moretti
- Frank DiMaio
- Jeremy Mills
- Yakov Kipnis
- Lei Shi
- Ray Wang
- Lucas Nivon
- Fabio Parmeggiani
- Matthew Smith
- Austin Day
- Possu Huang
- Olga Khersonsky
- Rie Koga
- Takahiro Kosugi
- Christy Tinberg
- Jiayi Dou
- Bonneau Lab
NYU - Richard Bonneau
- P. Douglas Renfrew
- Kevin Drew
- Evan Baugh
- Rebecca Alford
- Abba Leffler
- Leif Halvorsen
- Tim Craven
- Noah Youngs
- Das Lab
Stanford University - Rhiju Das
- Fang-Chieh Chou
- Karanicolas Lab
KU - John Karanicolas
- David Johnson
- Ragul Gowthaman
- Karen Khar
- Andrea Bazzoli
- Anatoly Ruvinsky
- Yan Xia
- Jimmy Budiardjo
- Havranek Lab
Washington University - Jim Havranek
- Ben Borgo
- Chi Zhang
- Kortemme Lab
UCSF - Tanja Kortemme
- Amelie Stein
- Roland Pache
- Yao-ming Huang
- Kyle Barlow
- Leo Gendelev
- Shane O'Connor
- Daniel Hoersch
- Kuhlman Lab
UNC - Brian Kuhlman
- Steven Lewis
- Tim Jacobs
- Andrew Leaver-Fay
- Ryan Hallett
- Joseph Harrison
- Bryan Der
- Matthew O'Meara
- Hayretin Yumerefendi
- Doo Nam Kim
- Seth Zimmerman
- Gray Lab
Johns Hopkins University - Jeff Gray
- Jianqing Xu
- Sergey Lyskov
- Brian Weitzner
- Daisuke Kuroda
- Krishna Praneeth Kilambi
- Nick Marze
- Will Proffitt
- Michael Pacella
- Julia Koehler Leman
- Meiler Lab
Vanderbilt University - Jens Meiler
- Liz Dong
- Sam DeLuca
- Stephanie DeLuca
- David Nannemann
- Joerg Schaarschmidt
- Steven Combs
- Amanda Duran
- Gordon Lemmon
- Jordan Willis
- Jessica Finn
- Yarov-Yarovoy Lab
UC Davis - Drew Tilley
- Phuong Nguyen
- Fleishman Lab
Weizmann Institute of Science, Israel - Sarel Fleishman
- Shira Warszawski
- Yearit
- Furman Lab
Hebrew University, Israel - Ora
- Michal
- Lior Zimmerman
- Orly Marcu
- Assaf Faragy
- Oliver Lange Lab
TU München - Oliver Lange
- Zhe Zhang
- Zaiyong Zhang
- Marcelino Arciniega Castro
- National Institute of Allergy and Infectious Diseases
- Xavier Ambroggio
- Andre Lab
Lund University, Sweden - Ingemar André
- Sebastian Rämisch
- Robert Lizatovic
- Bradley Lab
Fred Hutchinson Cancer Research Center - Phil Bradley
- Angela Liu
- Malmstroem Lab
IMSB, ETH Zurich - Abdullah Kahraman
- George Rosenberger
- Gront Lab
UW, Warsaw, Poland - Dominik Gront
- National Renewable Energy Lab
- Deanne Sammond
- Schief Lab
The Scripps Research Institute - Bill Schief
- Ron Jacak
- Dan Kulp
- Dunbrack Lab
Fox Chase Cancer Center - Roland Dunbrack
- Jared Adolf-Bryfogle
- Khare Lab
Rutgers - Sagar Khare
- Strauss Lab
Los Alamos National Lab - Charlie Strauss
- Ramesh Jha
- Rosetta Commons Guests
- Yeates Lab
UCLA - Todd Yeates
- Eisenberg Lab
UCLA - Luki Goldschmidt
- Keating Lab
MIT - Amy Keating
- Christopher Negron
- Vladimir Potapov
- Fraser Lab
UCSF - James Fraser
- de Groot Lab
Max Plank Institute for Biophysical Chemistry - Colin A. Smith
- Georgiou lab
University of Texas at Austin - Oana Lungu
- Li lab
City University of Hong Kong - Shuai Chen Li
- Ng lab
Universiti Tunku Abdul Rahman, Malaysia - Yen Kal Ng
- Richardson Lab
Duke - Daniel Keedy
- Liu Lab
China Three Gorges University - Sen Liu
- Hoecker Lab
Max-Planck Institute for Developmental Biology
Tuebingen, Germany - Andre C. Stiel
- PLoS ONE
- Rachel Bernstein
- Pande Lab
Stanford University - Gert Kiss
- ISB, WA
- Justin Ashworth
- Frimurer Lab
Copenhagen University, Denmark - Thomas Michael Frimurer
- Christoffer Norn