ROSETTA is a software suite for predicting and designing protein structures, protein folding mechanisms, and protein-protein interactions. ROSETTA has been consistently successful in CASP and CAPRI competitions.

http://www.rosettacommons.org/software/

RosettaAbinitio Performs de novo protein structure prediction.
RosettaDesign Identifies 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
RosettaSymmetry For enforcing symmetry in Rosetta
RosettaEnzdes For enzyme design
RosettaMembrane For membrane protein ab initio modeling
RosettaDDG For estimating the impact of sequence changes on protein stability
RosettaScripts An xml-based scripting language for controlling interface design, docking, and interface statistics
RosettaSnugDock Enables docking an antibody Fv region to an antigen and allows backbone flexibility in the paratope.