RosettaCon 2012 Tutorials

Tutorials are laid out in 4 rooms with three hour-long sessions each. Tutorials are organized by breadth of expected interest rather than theme.

Salmon Chapel: 140 seats
Woodpecker: 80+ seats (theater)
Nuthatch: 30+ seats (theater)
Flicker: 40+ seats (theater)

Here is a map that shows the layout of Sleeping Lady, http://www.sleepinglady.com/property-map.php

Table of contents

1 Session times

2 Salmon Chapel (main room)

3 Woodpecker

4 Flicker

5 Nuthatch

Session times: 3, 4, 5 PM

Salmon Chapel (main room)

Name	Title	Description	Audience	Session
Steven Lewis	Rosetta library structure and major classes	We'll dissect a relatively simple application (UBQ_E2_thioester or FloppyTail) and discuss what the major classes are, how they are used, and where they live.	Intended for the newest developers	slot 1 (3pm)
Sagar Khare	Protein design for ligand binding.	Starting from a given ligand target, a general protocol for designing proteins to bind it. Steps involve choosing globally shape complementary protein scaffolds, constructing idealized binding modes/networks, incorporating these binding modes in identified scaffold proteins, filtering and ranking resulting designs using various metrics. See Christy Tinberg's talk for an application of the method.	Rosetta users, some familiarity with RosettaScripts would be helpful	slot 2 (4pm)
Florian Richter	match + enzdes			slot 3 (5pm)

Woodpecker

Name	Title	Description	Audience	Session
Sergey Menis	How to identify potential scaffolds and transplant multiple discontinious regions using Multigraft	Multigraft (currently in Rosetta++ but is actively being migrated into Mini; Multigraft Match is already functional) has been successfully applied (here (http://bit.ly/KZk15f), here (http://bit.ly/KxDytS), here (http://bit.ly/KFEZ4R) and others) primarily to antibody epitope transplantation. However, the protocol allows for general transfer of discontinious protein backbone segments onto alternative scaffolds. We will go over potential uses and run the code.		slot 1 (3pm)
Matthew O'Meara	Feature Distribution Analysis: Bond Angles in Backrub Enembles	Features distribution analysis is a powerful framework to "unit test" structure predictions. To demonstrate, I will show how to compare bond-angle deviations in Backrub ensembles against bond-angle deviation in crystal structures.	Rosetta users	slot 2 (4pm)
Amelie Stein, Colin Smith	Flexible backbone design	We'll explain how to explore possible mutations and design computational libraries with the sequence tolerance protocol, using backrub-based ensembles as well as alternative ways to sample backbone flexibility. Also: discussion of the different parameters and how they may be varied depending on the input structure and research question, benchmarking, troubleshooting in case you see much more or less variation than expected.		slot 3 (5pm)

Flicker

Name	Title	Description	Audience	Session
Gordon Lemmon	Ligand docking using RosettaScripts.	LigandDocking with RosettaScripts is very flexible. Design your own protocol. Filter results at each step of docking protocol. Allow protein residues to redesign during docking. Simultaneously dock multiple small molecules, waters, metals, cofactors, etc.		slot 1 (3pm)
Lior Zimmerman, Assaf Faragy, Michal Sperber, Orly Marcu	Flexible peptide docking (FlexPepDock) and Flexible peptide binding prediction (FlexPepBind)	Starting from a peptide sequence and a receptor structure, we'll guide you through the process of modeling the interaction using several modeling applcations developed in our lab (FlexPepDock, FlexPepDock Ab-initio). That includes all the technical details of setting up the application as well as processing the output. We'll also give a brief introduction of a cool scheme that uses our flexible peptide modeling protocol to predict substrate specificity of different receptors (FlexPepBind).	Anyone who is interested in peptide-protein interactions and people who are interested in substrate specificity.	slot 2 (4pm)
Jason Labonte & Michael Pacella	How To Create Protocols & Movers To Do X in PyRosetta	This tutorial will demonstrate how one can use PyRosetta to create custom movers, protocols, and scoring methods that inherit from the respective C++ base classes for full integration into sequence & trial movers, etc. Also included: Tips for how to get the most out of Python and PyRosetta, such as: How to use the PyJobDistributor How to pass command line option flags Instruction on Rosetta functionality not covered in the PyRosetta user manual or workshops, such as: NMR constraints RNA Symmetry	all levels	slot 3 (5pm)

Nuthatch

Name	Title	Description	Audience	Session
Zaiyong Zhang	CS-Rosetta with NOE data using the automated setup;			slot 1 (3pm)
Zhe Zhang	replica exchange with rosetta-scripts and setting up a docking benchmark in automated Setup tools	This Tutorial will cover how to generalize the automated-setup to other protocol by subclass method implementation.	Intended for people who runs certain protocols on benchmarks	slot 2 (4pm)
Luki Goldschmidt	GPU acceleration of DARC	Getting started with GPU-izing of your code with OpenCL. Workshop will be based on GPU-izing DARC for virtual screening of ligands (with Karen Khar from John's lab).	advanced	slot 3 (5pm)

HACK