RosettaCon2008 Agenda

Tuesday - July 22nd (afternoon only)

1PM Introductions (< 10 min per lab)

3:30PM Session 1: "Rosetta Science" (Jeff Gray)

  Srivatsan Raman (Baker lab)
      High resolution protein refinement and the crystallographic phase problem
  Carie Fortenberry (Meiler lab)
      Design and Characterization of 2-Fold Symmetric TIM Barrels
  Eric Althoff (Baker lab)
      Computational enzymology: Hypotheses about success and failures in enzyme design

6-7PM Dinner

7:20PM After Dinner Keynote Lecture (David Baker)

7:50-9:50PM Concurrent sessions:

Poster Session I

Rosetta Tutorials I: "Rosetta Fundamentals" (Xavier Ambroggio)

  Xavier Ambroggio (RDG)
      A framework for understanding Rosetta
	-> Movies from Jens Meiler's website: protein folding (Ub), protein design (Top7) 
  Jenny Hu (Kuhlman Lab)
      Case Study: High-resolution design of a protein loop.
  Chu Wang (Baker Lab) and Glenn Butterfoss (Bonneau lab, RDG)
      Command lines and Options Session

9-11PM Drinks

Wednesday - July 23rd

7:30-8:30AM Breakfast

9AM Session 2: "Rosetta Science: Structure prediction" (Brian Kuhlman)

  David Masica (Gray lab)
      Solution and Adsorbed-State Ensembles of Biomineralization Proteins with RosettaSurface
  Rhiju Das (Baker lab)
      (Re)discovering missing physics in Rosetta, through RNA
  Kevin Drew (Bonneau lab)
      Protein Function Prediction Using Structural Homology
  Keith Henry (Meiler lab)
      Understanding amphetamines by modeling 
	the interaction of MDMA with the serotonin transporter from C. elegans

10:30AM Session 3: "Moving to Mini: Structure prediction" (Charlie Strauss)

  James Thompson (Baker lab)
      Comparative Modeling of Protein Structures
  Phil Bradley (Bradley lab)
      Predicting Protein-DNA Interaction Specificity
  Ian Davis (Baker lab)
      Ligand Docking with MiniRosetta
  Seth Cooper (Baker-affiliated)
      FoldIt

12:00-1PM Lunch

1:15PM Session 4: "Sampling techniques" (Bill Schief)

  Barak Raveh (Furman lab)
      PathRover: Sampling Dynamic Molecular Motion with Rosetta
  Colin Smith (Kortemme lab)
      Backrub news
  Dan Mandell (Kortemme lab)
      Kinematic Loop Closure & Flexible Backbone Interface Modeling

2:50PM Session 5: "Rosetta Science: Protein Design" (Phil Bradley)

  Jenny Hu (Kuhlman lab)
      Design of Beta Sheet Proteins
  Bruno Correia (Schief lab)
      HIV Immunogens Design - Targeting (Dis)continuous Motifs
  Nir London (Furman lab)
      OF rescuing MICE AND MEN: Structure-based computational design of superantigen inhibitors
  John Karanicolas (Baker lab)
      De Novo Design of Protein-Protein Interfaces

4:30PM Session 6: "Moving to Mini: Protein Design" (Rich Bonneau)

  Doug Renfrew (Kuhlman lab)
      Protein Design with Non-Canonical Amino Acids in MiniRosetta
  Paul Murphy (Baker lab)
      Alteration of Enzyme Specificity by Computational Loop Remodeling and Design
  Kristian Kaufmann (Meiler lab)
      Small Molecules as Rotamers: Generation and Docking in ROSETTALIGAND

6-7PM Dinner

7:20 After Dinner Keynote Lecture (Andrew Leaver-Fay)

7:50-9:50PM Concurrent sessions:

Poster Session II

Rosetta Tutorials II: "Select Protocols" (Xavier Ambroggio)

  Nir London (Furman-Schueler lab)
      So you've done docking. What now?
  Colin Smith (Kortemme lab)
      Simulating localized backbone flexibility with backrub moves

9-11PM Drinks

Thursday - July 24th

7:30-8:30AM Breakfast

9AM Session 7: "Mini: Technical Details and Discussion" (Tanja Kortemme)

  Chris Sheldahl (Snoeyink lab)
      Computational Experiments with a Lone-Pair Based Hydrogen-Bonding Potential in Mini
  Roland Dunbrack
      Smoothed high-resolution backbone-dependent rotamer libraries for protein structure prediction
  Steven Lewis (Kuhlman lab)
      Loop Modeling: Trimming the Fat The Job Distributor
  Sergey Lyskov (Gray lab)
      Testing infrastructure and procedures in Mini
  Yi Liu (Kuhlman lab)
      Discussion of Mini project release

12-1PM Lunch

1:15PM Session 8: "Interfaces to Rosetta" (Jens Meiler)

  Matt O'Meara (Kuhlman lab)
      Rosetta Design Wizard: Protein Design Through PyMol
  Will Sheffler (Baker lab)
      Pysetta? PyRosetta?

3:30PM Session 9: Macromolecular Modeling Outside of the Commons (Jens Meiler)

  Eric Drexler (Nanorex)
      Protein Engineering: Challenges and Applications for Composite Nanosystems
  Shaun Lippow (Codon Devices)
      Redesign of galactose oxidase substrate specificity
  Jeff Way (EMD Serono)
      Strand-Exchange Engineered Dimers: 
	A platform for multifunctional biotherapeutics and bispecific antibodies
  Deping Wang (Biogen Idec)
      Trying to Make Better Drugs with Molecular Modeling: 
	Structure-Guided Design of Therapeutic Antibodies
  Mark Sims (Nanorex)
      NanoEngineer-1:
	An open source multi-scale molecular modeling and simulation front-end for Rosetta

6-7PM Dinner

7:30-9PM Summary (aka Hike Organization)

RosettaCon 2008: Hikes

9-10PM PIs Meeting

Friday - July 25th

7:30-9AM Hike Departure!

RosettaCon 2008: Hikes

1:30PM Departure