RosettaScripts: A Scripting Language Interface to the Rosetta Macromolecular Modeling Suite

By Sarel Jacob Fleishman, Andrew Leaver-Fay, J. Corn, Eva-Maria Strauch, Sagar D. Khare, N. Koga, Justin Ashworth, Paul Murphy, Florian Richter, Gordon Lemmon and 2 more. 2011

614 citations recorded by the source corpus.

Macromolecular modeling and design are increasingly useful in basic research, biotechnology, and teaching. However, the absence of a user-friendly modeling framework that provides access to a wide range of modeling capabilities is hampering the wider adoption of computational methods by non-experts. RosettaScripts is an XML-like language for specifying modeling tasks in the Rosetta framework. RosettaScripts provides access to protocol-level functionalities, such as rigid-body docking and sequence redesign, and allows fast testing and deployment of complex protocols without need for modifying or recompiling the underlying C++ code. We illustrate these capabilities with RosettaScripts protocols for the stabilization of proteins, the generation of computationally constrained libraries for experimental selection of higher-affinity binding proteins, loop remodeling, small-molecule ligand docking, design of ligand-binding proteins, and specificity redesign in DNA-binding proteins.

Subfields: Materials Chemistry, Molecular Biology

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Citations in the corpus

Improving homology modeling from low-sequence identity templates in Rosetta: A case study in GPCRs (2020, methodology): “Threaded models were passed to the hybridization application via use of Rosetta XML scripts [23,32].”
Scientific Benchmarks for Guiding Macromolecular Energy Function Improvement (2013, methodology): “Once a batch and relevant feature reporters (Table 6.1) have been selected, the features are extracted to the database using the ReportToDB mover in the RosettaScripts XML-based protocol language (Fleishman et al., 2011).”
Protein sequence design by conformational landscape optimization (2021, methodology): “Backbones were constructed using blueprints (29) with distance and angle constraints to guide the formation of β -sheet backbone hydrogen bonds (30), followed by sequence design with Rosetta [FastDesign (28, 31) in conjunction with LayerDesign (21) and using the Rosetta all-atom energy function (32)”
Diffusion probabilistic modeling of protein backbones in 3D for the motif-scaffolding problem (2022, neutral): “Another class of methods, referred to as fixed backbone sequence design [12, 20, 40, 27, 18], attempts to solve the problem of identifying a sequence that folds into any given designable backbone structure.”
Assessing and enhancing foldability in designed proteins (2021, methodology): “RosettaScripts [42] and commandlines are available through github https://github.”
Improvements to Robotics-Inspired Conformational Sampling in Rosetta (2013, methodology): “framework [48] on the starting structures used for KIC and NGK simulations.”
Assessment and Challenges of Ligand Docking into Comparative Models of G-Protein Coupled Receptors (2013, methodology): “Ligand docking into the comparative models was performed with Rosetta Scripts [37–40] (Figure 1, Step 8).”
Efficient Flexible Backbone Protein-Protein Docking for Challenging Targets (2017, methodology): “To generate diversity in backbone conformations for the RosettaDock 4.0 runs, we used three conformer generation meth-ods: perturbation of the backbones along the normal modes by 1A˚ et al. , 2001) [using RosettaScripts (Fleishman et al. , 2011)], refinement using the Relax protocol in Rosetta (Tyka”
Designing Peptides on a Quantum Computer (2019, methodology): “We classically sampled 16-residue peptide macrocycle α-sheet backbone conformations using a protocol developed in the RosettaScripts scripting language ( 39 ) , then carried out design on the quantum annealer.”