Macromolecular Modeling Blog ™

Rosetta 3.0 was release on the Rosetta Commons website last Friday, February 27th.  Rosetta 3.0 is a whole new Rosetta developed in a purely object oriented manner.  Most functionality from previous versions of Rosetta have been ported over and tested, ensuring very similar results.  Rosetta 3.0 is available for download as a BETA version and any users are encouraged to give feedback.

A big improvement over previous versions of Rosetta is the ability to create custom “apps”, as well as compile existing and documented apps as separate executables.  Gone are the days of a single executable all modes with a paragraph worth of flags.  Now, each app has its own executable and flags.

Existing apps that can be compiled and run with no modifications include:

RosettaAbinitio – Performs de novo protein structure prediction.

RosettaDesign – Dentifies low free energy sequences for target protein backbones.

RosettaDesign pymol plugin – A user-friendly interface for submitting Protein Design simulations using RosettaDesign.

RosettaDock – Predicts the structure of a protein-protein complex from the individual structures of the monomer components.

RosettaAntibody – Predicts antibody Fv region structures and performs antibody-antigen docking.

RosettaFragments – Generates fragment libraries for use by Rosetta ab initio in building protein structures.

RosettaNMR – Incorporates NMR data into the basic Rosetta protocol to accelerate the process of NMR structure prediction.

RosettaDNA – For the design of proteins that interact with specified DNA sequences.

RosettaRNA – Fragment assembly of RNA.

RosettaLigand – For small molecule – protein docking.