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...

The Rosetta molecular modeling software package provides experimentally tested and rapidly evolving tools for the 3D structure prediction and high-resolution design of proteins, nucleic acids, and a growing number of non-natural polymers. Despite its free availability to academic users and improving documentation, use of Rosetta has largely remained confined to developers and their immediate co...

The Rosetta Molecular Modeling suite is a command-line-only collection of applications that enable high-resolution modeling and design of proteins and other molecules. Although extremely useful, Rosetta can be difficult to learn for scientists with little computational or programming experience. To that end, we have created a Graphical User Interface (GUI) for Rosetta, called the PyRosetta Tool...

The objective of this review is to enable researchers to use the software package Rosetta for biochemical and biomedicinal studies. We provide a brief review of the six most frequent research problems tackled with Rosetta. For each of these six tasks, we provide a tutorial that illustrates a basic Rosetta protocol. The Rosetta method was originally developed for de novo protein structure predic...

The Rosetta macromolecular modeling software is a versatile, rapidly developing set of tools that are now being routinely utilized to address state-of-the-art research challenges in academia and industrial research settings. A Rosetta Conference (RosettaCon) describing updates to the Rosetta source code is held annually. Every two years, a Rosetta Conference (RosettaCon) special collection desc...

We introduce Rosetta, a program allowing for the translation between different bases of effective field theory operators. We present the main functions of the program and provide an example of usage. One of the Lagrangians which Rosetta can translate into has been implemented into FeynRules, which allows Rosetta to be interfaced into various high-energy physics programs such as Monte Carlo even...

Rosetta is a systems level design language that allows algebraic specification of systems through facets. The usual approach to formally describe a specification is to define an algebra that satisfies the specification. Although it is possible to formally describe Rosetta facets with the use of algebras, we choose to use the dual of algebra, i.e. coalgebra, to do so. Coalgebras are particularly...

A policy is a statement that an action is permitted or forbidden if certain conditions hold. We introduce a language for reasoning about policies called Rosetta. What makes Rosetta different from existing approaches is that its syntax is essentially a fragment of English. The language also has formal semantics, and we can prove whether a permission follows from a set of Rosetta policies in poly...

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...

We have developed an approach for determining NMR structures of proteins over 20 kDa that utilizes sparse distance restraints obtained using transverse relaxation optimized spectroscopy experiments on perdeuterated samples to guide RASREC Rosetta NMR structure calculations. The method was tested on 11 proteins ranging from 15 to 40 kDa, seven of which were previously unsolved. The RASREC Rosett...