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

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New features of the current release (Rosetta 3.2)

Comparative Modeling: This application build structural models of proteins using one or more known structures as templates for modeling.

Flexible Peptide Docking: This application is designed to create high-resolution models of complexes between flexible peptides and globular proteins, starting from approximate, coarse-grain models.

Symmetric Docking: This application predicts 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: The matcher application can 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: This application is to be used for solving difficult molecular replacement problems. It will generally be used alongside the molcular replacement software Phaser.

Sequence Tolerance: The general uses of this application are specificity prediction and library design (i.e. for phage display, yeast display, or other selection techniques

Software Functionality Summary

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.

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