ROSETTA Technical Reference Manual ∗

Real-Time PyMOL Visualization for Rosetta and PyRosetta

Computational structure prediction and design of proteins and protein-protein complexes have long been inaccessible to those not directly involved in the field. A key missing component has been the ability to visualize the progress of calculations to better understand them. Rosetta is one simulation suite that would benefit from a robust real-time visualization solution. Several tools exist for...

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Rosetta energy terms used in energy calculations The contribution towards fold stability (ERESFold) of each mutated residue i at each sequence position j was estimated by recording the sum of interand intra-residue Rosetta energy terms: ERESFold, i,j = E_LJatr (i,j) + E_LJrep (i,j) + G_sol (i,j) + E_dun (i,j) + E_hb (i,j) + E_prob (i,j) + E_pair (i,j) – E_ref (i,j), where: E_LJatr: attractive c...

PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta

SUMMARY PyRosetta is a stand-alone Python-based implementation of the Rosetta molecular modeling package that allows users to write custom structure prediction and design algorithms using the major Rosetta sampling and scoring functions. PyRosetta contains Python bindings to libraries that define Rosetta functions including those for accessing and manipulating protein structure, calculating ene...

Accurate Automated Protein NMR Structure Determination Using Unassigned NOESY Data

Conventional NMR structure determination requires nearly complete assignment of the cross peaks of a refined NOESY peak list. Depending on the size of the protein and quality of the spectral data, this can be a time-consuming manual process requiring several rounds of peak list refinement and structure determination. Programs such as Aria, CYANA, and AutoStructure can generate models using unas...

The NorduGrid / ARC Information System Technical Description and Reference Manual