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













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

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: Finding/Starting an Academic Position (Mentors: Firas Khatib, Chu Wang, Birte Hocker, Justin Siegel)

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


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.

 
     


backbone

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.

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Industry Participants


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

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Academic Participants


  • RosettaCommons

  • Baker Lab
    UW
  • David Baker
  • Aaron Chevalier
  • Alex Ford
  • Austin Day
  • Cassie Bryan
  • Christopher Bahl
  • Daniel Silva
  • David Kim
  • Eva-Maria Strauch
  • Fabio Parmeggiani
  • Gabriel Rocklin
  • George Ueda
  • Javier Caste
  • Jorge Fallas
  • Jorgen Nelson
  • Lei Shi
  • Luki Goldschmidt
  • Patrick Conway
  • Scott Boyken
  • Shane Gonen
  • TJ Brunette
  • Una Nattermann
  • Yifan Song
  • Ariel Ben-Sasson
  • David La
  • Hahnbeom Park
  • Jiayi Dou
  • Neil King
  • Gustav Oberdorfer
  • Yuan Liu
  • Enrique Marcos
  • Rashmi Ravichandran
  • Possu Huang
  • Chunfu Xu
  • Sergey Ovchinnikov

  • Bonneau Lab
    NYU
  • Richard Bonneau
  • Doug Renfrew
  • Evan Baugh
  • Abba Leffler
  • Kevin Drew
  • Andrew Watkins
  • Noah Youngs
  • Riley Simmons-Edler
  • Emily Koo
  • Kevin Drew

  • Das Lab
    Stanford CA
  • Rhiju Das
  • Joseph Yesselman
  • Clarence Cheng

  • Dunbrack Lab
    FCCC
  • Roland Dunbrack
  • Jared Adolf-Bryfogle
  • Maxim Shapovalov
  • Vivek Modi
  • Qifang Xu

  • Khatib Lab
    U Mass Dartmouth
  • Firas Khatib
  • Anand Shah

  • Kortemme Lab
    UCSF
  • Tanja Kortemme
  • Amanda Loshbaugh
  • Kale Kundert
  • Kyle Barlow
  • Pradeep Bandaru
  • Samuel Thompson
  • Tanja Kortemme
  • Tina Perica
  • Yao-ming Huang
  • Shane O'Connor

  • Khare Lab
    Rutgers
    U
  • Sagar Khare
  • Beidi Lu
  • Kenny Kostenbader
  • Lu Yang
  • Srinivas Annavarapu

  • Kuhlman Lab
    UNC
  • Brian Kuhlman
  • Andrew Leaver-Fay
  • Doo Nam Kim
  • Joseph Harrison
  • Kevin Houlihan
  • Ryan Hallett
  • Sharon Guffy
  • Tim Jacobs

  • Havranek Lab
    Washington U
  • Jim Havranek
  • Adam Joyce
  • Chi Zhang
  • Benjamin Borgo

  • Gray Lab
    Johns Hopkins University
  • Jeffrey Gray
  • Jason Labonte
  • Julia Koehler
  • Nicholas Marze
  • Rebecca Alford
  • Brian Weitzner
  • Sergey Lyskov
  • Michael Pacella
  • Shourya Sonkar Roy Burman

  • Meiler Lab
    Vanderbilt University
  • Jens Meiler
  • Alyssa Lokits
  • Amanda Duran
  • Brittany Allison
  • Darwin Fu
  • Jens Meiler
  • Rocco Moretti
  • Alex Sevy
  • Yan Xia
  • Steven Combs
  • Thomas Charles Willcock
  • Sandeepkumar Kailas

  • Barth Lab
    Baylor College of Medicine
  • Patrick Barth
  • Yumeng Wang
  • Xiang Feng

  • Fleishman Lab
    Weizmann Institute of Science
  • Sarel Fleishman
  • Assaf Alon
  • Dror Baran
  • Gideon Lapidoth
  • Olga Khersonsky
  • Christoffer Norn
  • Adi Goldenzweig
  • Shira Warszawski

  • Furman Lab
    Hebrew University
  • Ora Schueler-Furman
  • Yuval Sedan
  • Nawsad Alam
  • Emma Joy Dodson
  • Orly Marcu

  • Lange Lab
    TU München
  • Oliver Lange
  • Justin Porter
  • Tatjana Braun
  • Zhe Zhang

  • Richardson Lab
    Duke University
  • Jane Richardson
  • Steven Lewis

  • Yarov-Yarovoy Lab
    UC Davis
  • Vladimir Yarov-Yarovoy
  • Drew Tilley
  • Jon Sack
  • Phuong Nguyen
  • Fan Yang

  • Schief Lab
    Scripps Research Institute
  • Name
  • Bill Schief
  • Joe Jardine
  • Dan Kulp
  • Sergey Menis
  • Shantanu Bhattacharyya

  • Rosetta Design Group
  • Xavier Ambroggio

  • Karanicolas Lab
    KU
  • John Karanicolas
  • Andrea Bazzoli
  • David Johnson
  • John Karanicolas
  • Karen Khar
  • Ragul Gowthaman
  • Shipra Malhotra
  • Simon Kelow

  • DiMaio Lab
  • Frank DiMaio
  • Ray Wang

  • Wang Lab
    Peking U
  • Chu Wang

  • Siegel Lab
    UC Davis
  • Justin Siegel
  • Steve Bertolani
  • James Lucas
  • Alex Carlin

  • Strauss Lab
    Los Alamos National Lab
  • Charlie Strauss
  • Hossein Fazelinia
  • Ramesh Jha

  • Bax Lab
    NIH
  • Nikolaos Sgourakis

  • Malmstroem Lab
    ETH Zurich
  • Lars Malmstroem

  • Whitehead Lab
    Michigan State
  • Tim Whitehead
  • Justin Klesmith
  • Carolyn Haarmeyer

  • National Renewable Energy Lab
  • Deanne Sammond

  • Andre Lab
    Lund U
  • Ingemar Andre
  • Sebastian Rämisch
  • Wojciech Potrzebowski
  • Marie Sofie Moeller

  • Gront Lab
    U of Warsaw
  • Dominik Gront
  • Agata Szczasiuk
  • Aleksandra El bieta Dawid
  • Lukasz Wieteska
  • Marta Strumillo

  • Bradley Lab
    FHCRC
  • Philip Bradley

  • Bystroff Lab
    RPI
  • Chris Bystroff
  • Christian Schenkelberg
  • Shounak Banerjee

  • RosettaCommons Guests

  • Hein Wijma (U Groningen)
  • Annemarie Honegger (UZH)
  • Julia Shifman (HU)
  • Andrej Sali (UCSF)
  • Nir London (UCSF)
  • Colin Smith (Max Planck)
  • Birte Höcker (Max Planck)
  • Elizabeth Kellogg (UC Berkeley)
  • Kala Bharath Pilla (ANU)
  • Oana Lungu (UT Austin)
  • Michelle Dohm (PLoS ONE)
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