New features of the current release (Rosetta 3.4)
Point mutant scan application: The purpose of this protocol is to increase the stability of a protein of interest with only single or double point mutants.
Non canonical amino acid utilities: This feature includes 2 applications: 1) MakeRotLib - This application creates a noncanonical amino acid rotamer library and 2)UnfoldedStateEnergyCalculator - This application calculates the explicit unfolded state energies.
RNA assembly with experimental pair-wise constraints: This code is intended to take an RNA sequence and secondary structure and then give three-dimensional de novo models of the helices and inter-helical motifs, and then build up the complete model from these parts.
RNA 3D structure modeling: Added the applications: rna_cluster, rna_minimize and rna_helix
RNA loop modeling with stepwise assembly: This method builds single-stranded RNA loops using a deterministic, enumerative sampling method called Stepwise Assembly.
Remodeling RNA crystallographic models with electron density constraint: This code is used for improving a given RNA crystallographic model and reduce the number of potential errors in the model (which can evaluated by Molprobity), under the constraint of experimental electron density map.
Chemically conjugated docking : These extensions of the UBQ_E2_thioester protocol allow modeling of
chemically conjugated proteins (such as ubiquitin tagged to a target)
via isopeptide, thioester, and disulfide linkages.
RosettaVIP void identification and packing application: This code is intended to take a pdb file with the coordinates for a structural model of a protein with poor hydrophobic packing, and to return a list of mutations that are predicted to fill cavities in the protein core.
Relax pdb with allatom constraints: hese scripts relax a pdb (minimize rosetta score) while keeping atoms as close as possible to the original positions in the crystal. It is designed to be used to prepare a structure for subsequent design in rosetta.
Beta strand homodimer design: This code was written for a relatively singular application: finding proteins with surface exposed beta-strands, then trying to make and design a homodimer that will form via that beta-strand.
DougsDockDesignMinimizeInterface: This protocol was used in the accompanying manuscript to redesign the protein/peptide interface of Calpain and a fragment of its inhibitory peptide calpastatin.
