Materials for “Protocols for Molecular Modeling with Rosetta3 and RosettaScripts.” (2016)

These are the complete tutorials (including all input files and example output files) for the protocols presented in Bender et al. “Protocols for Molecular Modeling with Rosetta3 and RosettaScripts.” Biochemistry 2016. These tutorials are written to work with the Rosetta 3.6 release, using the updated talaris2014 energy function. Users of Rosetta 3.8 or later may need to use the Rosetta/tools/xsd_xrw/ script to convert the provided XMLs into the updated format. These tutorials contain step-by-step instructions for worked examples of the given protocol. A version of the tutorials with just the essential input files can be found as Supporting Information on the Biochemistry website.

Main Tutorials:

Tutorial 1: Ab initio Folding
Tutorial 2: Comparative Modeling
Tutorial 3: Protein-Protein Docking
Tutorial 4: Ligand Docking
Tutorial 5: Protein Design
Tutorial 6: Structure Refinement with Electron Density

Additional Materials:

Tutorial 1: Scoring and preparation
Tutorial 2: Clustering with Calibur