Rosetta/MDFF Tutorial

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University of Illinois at Urbana-Champaign
Beckman Institute for Advanced Science and Technology
Theoretical and Computational Biophysics Group
Computational Biophysics Workshop

Interactive Model Building with ModelMaker

ModelMaker Developers:
Till Rudack
Maximillian Scheurer
Ryan McGreevy

Tutorial by Maximilian Scheurer, Till Rudack, Marc Siggel, Ryan McGreevy, João Ribeiro, and Justin R. Porter

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Contents
Introduction
Required software
Folding protein termini using ModelMaker
- Structure prediction
- Interactive fitting to a cryo-EM density with iMDFF and QwikMD
Modeling amino acid insertions
- Structure prediction with Rosetta
- Interactive fitting to a cryo-EM density with iMDFF
Model fit to mid-resolution EM density
Homology model
High-resolution real-space refinement