Macromolecular modeling and design in Rosetta: recent methods and frameworks

Abstract

The Rosetta software suite for macromolecular modeling, docking, and design is widely used in pharmaceutical, industrial, academic, non-profit, and government laboratories. Despite its broad modeling capabilities, Rosetta remains consistently among leading software suites when compared to other methods created for highly specialized protein modeling and design tasks. Developed for over two decades by a global community of over 60 laboratories, Rosetta has undergone multiple refactorings, and now comprises over three million lines of code. Here we discuss methods developed in the last five years in Rosetta, involving the latest protocols for structure prediction; protein-protein and protein-small molecule docking; protein structure and interface design; loop modeling; the incorporation of various types of experimental data; modeling of peptides, antibodies and proteins in the immune system, nucleic acids, non-standard chemistries, carbohydrates, and membrane proteins. We briefly discuss improvements to the energy function, user interfaces, and usability of the software. Rosetta is available at www.rosettacommons.org.

An enumerative algorithm for de novo design of proteins with diverse pocket structures

“…De novo protein design is a two-step process: First, a protein backbone conformation is generated, and second, low-energy amino acid sequences for this backbone are found by combinatorial side-chain packing calculations. In Rosetta ( 12 , 13 ), new backbones can be constructed by Monte Carlo assembly of short peptide fragments based on a structure “blueprint,” which describes the length of the secondary structure elements, strand pairings, and backbone torsion ranges for each residue ( 14 , 15 ). Because this process is stochastic, each structure generated is distinct.…”

How HIV-1 Integrase Associates with Human Mitochondrial Lysyl-tRNA Synthetase

“…In parallel to the identification of the residues involved in the interaction between IN-CTD and mLysRS by experimental methods, we set up an independent docking simulation to explore the most likely interface which could be identified using the InterEvDock2 server [ 27 ] and a refinement protocol based on Rosetta software [ 34 ] (see Mat & Met). We did not use any of the experimental constraint a priori to guide the docking.…”

“…Models were clustered using fcc [ 33 ] with a cutoff threshold of 0.5 and removing similarities between symmetrical structures. Forty-nine non-redundant representative models of complexes were retrieved and were refined using Rosetta [ 34 ] through a standard relax protocol under native coordinate constraints and the scoring of the resulting interface energy between IN-CTD and LysRS using the beta_nov15 scoring function. The model with the lowest interface energy reached −45.9 rosetta units, significantly lower than any of the alternative configurations (second best model at −41.3) and was first selected for in-depth structural analysis and design of disruptive compensatory mutants.…”

Receptor-free Discrimination of Peptide Native Bound Conformations Suggests Limited Transferability of the “cen_std+score4l” Rosetta Energy Function From Proteins to Peptides

“…In this work we have reported on the ability of the Rosetta cen_std+score4L energy function to discriminate in favor of such native conformations. Rosetta is a popular macromolecular modeling suite [31] that has been successfully used in modeling tasks that range from protein structure prediction [58] to the design of high-affinity protein binders [59] to the docking of small molecules [60] and peptides [10]. While Rosetta has a default energy function for high-resolution modeling [32], each modeling task performed at low resolution must explicitly specify its own energy function.…”

“…In the Rosetta macromolecular modeling software suite [31], a scoring, or "energy", function is a linear combination of terms that capture energetic contributions of different physical nature. This functional form is used under both of Rosetta's resolution modes, namely, the "fullatom" mode, where all atoms of the biomolecule are explicitly represented [32], and the "centroid" mode, where nonpolar hydrogens are neglected and side-chain atoms beyond C β are represented by a single pseudo-atom (the centroid) located in an idealized center of mass [33].…”