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/rewrite_rosetta_script.py 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 Text (pdf)
• Full Tutorial (zip)

Tutorial 2: Comparative Modeling

• Tutorial Text (pdf)
• Full Tutorial (zip)

Tutorial 3: Protein-Protein Docking

• Tutorial Text (pdf)
• Full Tutorial (zip)

Tutorial 4: Ligand Docking

• Tutorial Text (pdf)
• Full Tutorial (zip)

Tutorial 5: Protein Design

• Tutorial Text (pdf)
• Full Tutorial (zip)

Tutorial 6: Structure Refinement with Electron Density

• Tutorial Text (pdf)
• Full Tutorial (zip)

Additional Materials:

Tutorial 1: Scoring and preparation

• Tutorial Text (pdf)
• Full Tutorial (zip)

Tutorial 2: Clustering with Calibur

• Tutorial Text (pdf)
• Full Tutorial (zip)