Manual

The latest weekly release is Rosetta 2014wk05

New features of Rosetta 3.5

Major updates to relational database support

Many new Movers, Filters, TaskOperations, etc

NGK "Next Generation" kinematic loop closure

Updates to chemically_conjugated_docking apps UBQ_E2_thioester and neighbors (Saha A, Kleiger G, Lewis S, Kuhlman B, Deshaies RJ. Essential role for ubiquitin-ubiquitin-conjugating enzyme interaction in ubiquitin discharge from Cdc34 to substrate. Molecular Cell. In press.)

LOOP_DEFINITIONS tag Loop specification within RosettaScripts

OUTPUT tag Rescore-on-output option for RosettaScripts

ERRASER package for RNA structure correction with or without experimental electron density (NOTE: collaboration with the PHENIX project; requires PHENIX liscenced and installed separately).

ResourceManager allows for different command-line arguments and other centrally-managed resources with different jobs within one instantiation of Rosetta 

OpenCL support - notice only a very few algorithms feature GPU support; general GPU support is not yet present. previous CUDA support removed

Updates to the FloppyTail app

pmut_scan app upgraded to have support for Rosetta++ alter_spec mode - it scans for destabilizing rather than stabilizing mutations (particularly at protein-protein interfaces)

Linear Memory Interaction Graph now works with symmetric poses

Enzyme design at protein-protein interfaces

Supercharge application (Lawrence MS, Phillips KJ, Liu DR. Supercharging proteins can impart unusual resilience. J Am Chem Soc. 2007 Aug 22;129(33):10110-2.)

 

3x1 metal-mediated interface design application (Der BS, Machius M, Miley MJ, Mills JL, Szyperski T, Kuhlman B. Metal-mediated affinity and orientation specificity in a computationally designed protein homodimer. J Am Chem Soc. 2012 Jan 11;134(1):375-85.)

New demos ERRASER, favor_native_residue, Protocol captures

Scoring

-use_bicubic_interpolation smooths issues with binned knowledge-based

phi-psi based terms (including Ramachandran, p_aa_pp, and Dunbrack
(2002 only)
centroid radii bugfixes
New RNA scoring potentials, for use with ERRASER and PHENIX
-analytic_etable_evaluation (affects fa_rep, fa_atr, fa_sol, fa_intra_rep) offers a major memory reduction and removes a derivative discontinuity, at the cost of some speed
sasapack and avge scores from Rosetta++
Dunbrack 2010 (Dun10) library added. Dunbrack 2008 (Dun08) library deprecated and removed. Note that Dun10 is only available to academic users as part of the Rosetta download at this time; Dun10 must be separately liscenced for commercial users (LINKY).  Feel free to contact us via the forums for assistance in installing the Dun10 library.
lbfgs minimizer - more efficient for minimization with many DOFs, especially Relax
cartesian minimizer - allows minimization of 3D coordinates instead of internal torsions, including minimization of bond lengths and angles
-bbdep_omega - backbone-dependent omega torsion scoring term

Tools

Python scripts for Rosetta output processing (turning scorefiles into score v. RMSD plots, etc.)

pdb2vall package - generates a VALL fragment_picker template database from a specified PDB+chain

batch_molfile_to_params.py - used for creating large numbers of ligand paramter files (for virtual screening, etc.), script to load silent files directly into PyMOL.