Rosetta 3.2 is the first rosetta release in over a year and is chock-full of new features. Get your (free for academia) copy at: www.rosettacommons.org/software and find the new and improved documentation at: www.rosettacommons.org/manuals/archive/rosetta3.2_user_guide
What’s new in Rosetta 3.2 ?
“Automatic” Comparative Modeling: build structural models of proteins using one or more known structures as templates for modeling.
Flexible Peptide Docking: create high-resolution models of complexes between flexible peptides and globular proteins, starting from approximate, coarse-grain models.
Symmetric Docking: predict the structure of symmetric homooligomeric protein assemblies starting from the structure of a single subunit. The relative subunit orientation and conformations of side-chains are simultaneously optimized for a symmetric protein assembly.
RosettaMatch Application: search through a protein backbone (“scaffold”) to find positions where a binding site for a desired small molecule (or biomolecule, in the more general case) target can be introduced.
Molecular Replacement: solve difficult molecular replacement problems. It will generally be used alongside the molecular replacement software Phaser.
Sequence Tolerance: perform specificity prediction and library design (i.e. for phage display, yeast display, or other selection techniques).