The PyRosetta Toolkit: a graphical user interface for the Rosetta software suite

Abstract

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 Toolkit, for creating and running protocols in Rosetta for common molecular modeling and protein design tasks and for analyzing the results of Rosetta calculations. The program is highly extensible so that developers can add new protocols and analysis tools to the PyRosetta Toolkit GUI.

Figure 1. PyRosetta Toolkit GUI.

Top-Left: Energy and RMSD analysis functions. Bottom-Left: Region selection. Top-Right: Output options. Bottom-Right: Decoy and Protocol options as well as some common modeling protocols.

Figure 2. Rosetta Flag File Builder.

Top-Left: All Rosetta applications found in a user-specified directory. Top-Middle: All options parsed from Rosetta Doxygen documentation housed in rosetta_source. Clicking an option gives a description, if any is found, in the textbox on the right. Bottom-Middle: Text window that functions in building a config file. Adding an option will add it to this textbox, while the PathBuilder allows users to search for various files and add them to the textbox. Right: Information textbox which gives information on individual options as well as each major component of Rosetta Doxygen documentation (Purpose, Unparsed Options, Code and Demo, References, Algorithm, Limitations, Modes, Input Files, Tips, Expected Outputs, and Post Processing).

Figure 3. Score Function Control and Creation.

Top: All score function weights and patch files found in the Rosetta chemical database. These weights and patches can be set as the current GUI score function or saved as the default. Bottom-Left: Terms in the current score function and their associated weights. Weights can be changed by double-click. Bottom-Right: All Rosetta energy terms can be enabled at a certain weight by double-click.

Figure 4. Design – Setup Resfile.

Left: A resfile for design is constructed for individual residues or stretches of residues. Biochemical data is given for each current residue. Right: Selections of residue types. Once selected, individual residues in the category are added to the box on the right. Added residues are found in the lower box, where the current designable residues can be edited or cleared.

Figure 5. Ligand/NCAA/PTM Manager.

Top: Selection is grouped first by patch/ligand/polymer, then by specific biochemical property. Middle: Rosetta related information is given about the particular selection. Bottom: Functions for optimizing the current energy function for use with ligands, non-canonical amino acids (NCAA), and post-translational modifications (PTM).

Figure 6. Per-Residue Control and Analysis.

A collection of functions for analyzing, modeling, and designing individual residues. Per-residue energies, probabilities, and dihedral angles are given. Variants may be added or removed from residues, any residue may be designed or mutated, and individual rotamers may be optimized.