Serverification of Molecular Modeling Applications: The Rosetta Online Server That Includes Everyone (ROSIE)

By Sergey Lyskov, Fang-Chieh Chou, Shane Ó Conchúir, Bryan S. Der, K. Drew, Daisuke Kuroda, Jianqing Xu, Brian D. Weitzner, P. Renfrew, Parin Sripakdeevong and 7 more. 2013

417 citations recorded by the source corpus.

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 collaborators due to the code’s difficulty of use, the requirement for large computational resources, and the unavailability of servers for most of the Rosetta applications. Here, we present a unified web framework for Rosetta applications called ROSIE (Rosetta Online Server that Includes Everyone). ROSIE provides (a) a common user interface for Rosetta protocols, (b) a stable application programming interface for developers to add additional protocols, (c) a flexible back-end to allow leveraging of computer cluster resources shared by RosettaCommons member institutions, and (d) centralized administration by the RosettaCommons to ensure continuous maintenance. This paper describes the ROSIE server infrastructure, a step-by-step ‘serverification’ protocol for use by Rosetta developers, and the deployment of the first nine ROSIE applications by six separate developer teams: Docking, RNA de novo, ERRASER, Antibody, Sequence Tolerance, Supercharge, Beta peptide design, NCBB design, and VIP redesign. As illustrated by the number and diversity of these applications, ROSIE offers a general and speedy paradigm for serverification of Rosetta applications that incurs negligible cost to developers and lowers barriers to Rosetta use for the broader biological community. ROSIE is available at http://rosie.rosettacommons.org.

Subfields: Materials Chemistry, Molecular Biology

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Citations in the corpus

Modeling complex RNA tertiary folds with Rosetta. (2015, background): “…of submotifs (up to 30 nucleotides) of a large RNA can also be carried out freely through the Rosetta Online Server that Includes Everyone (ROSIE, http://rosie.rosettacommons.org) (Lyskov et al., 2013), and, if desired, these submodels can be integrated into larger models (see Section 3.6).”
FARFAR2: Improved de novo Rosetta prediction of complex global RNA folds (2020, positive): “First, we describe how improvement of the general Rosetta codebase as well as consolidation of the FARFAR protocol have enabled development of a streamlined version of the method, named FARFAR2, and an improved webserver on the ROSIE platform (Lyskov et al., 2013; Moretti et al., 2018) at https://ro”
Selectivity by Small-Molecule Inhibitors of Protein Interactions Can Be Driven by Protein Surface Fluctuations (2015, positive): “In addition to the command-line program included in Rosetta, we have provided a tool to generate an exemplar from an input PDB file through the ROSIE web interface (165).”
Computing structure-based lipid accessibility of membrane proteins with mp_lipid_acc in RosettaMP (2016, methodology): “We further provide a publicly accessible webserver to run the classification, which is implemented in the ROSIE environment [25], accessible at http://rosie.graylab.jhu.edu/mp_lipid_acc/ submit.”
InteractiveROSETTA: a graphical user interface for the PyRosetta protein modeling suite (2015, background): “Rosie (Rosetta Online Server that Includes Everyone) provides access to computational resources for big Rosetta jobs (Lyskov et al. , 2013).”
Modeling and docking antibody structures with Rosetta (2017, background): “Run the cluster identification application as follows: identify_cdr_clusters.macosclangrelease\ –s grafting/model-*.relaxed.pdb\ – out:file:score_only north_clusters.log North et al. clustered all CDR loop structures by their backbone dihedral angles and named them by CDR type, loop length and clust”
RNA Structure Refinement using the ERRASER-Phenix pipeline (2013, methodology): “This chapter describes the details of using ERRASER in three easily accessible ways: by a GUI in the Phenix package, from the command-line, and with the ROSIE server (13).”
Web‐accessible molecular modeling with Rosetta: The Rosetta Online Server that Includes Everyone (ROSIE) (2018, methodology): “35 Here, we describe an improvement to the application program interface (API) for the ROSIE framework.”
Peptiderive server: derive peptide inhibitors from protein–protein interactions (2016, methodology): “In order to make it widely accessible to the community, we have developed a web server for Peptiderive within the framework of the ROSIE (Rosetta Online Server that Includes Everyone) web interface for Rosetta protocols (21).”
Better together: Elements of successful scientific software development in a distributed collaborative community (2020, methodology): “In 2013, the ROSIE server framework[64] was created to simplify setting up new webservers for Rosetta applications.”
Improved prediction of antibody VL-VH orientation. (2016, methodology): “The MT protocol is available on the ROSIE public Web server (rosie.graylab.jhu.edu, Lyskov et al., 2013) as an option of the Antibody homology modeling protocol.”