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

Sarel J Fleishman,Andrew Leaver-Fay,Eva-Maria Strauch,Justin Ashworth,Jacob E Corn,David Baker,Paul Murphy,Jens Meiler,Gordon Lemmon,Florian Richter,Sagar D Khare,Nobuyasu Koga

doi:10.1371/journal.pone.0020161

Abstract

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.

Highlights

The Rosetta software suite for macromolecular modeling has useful applications in many areas of interest to molecular biologists
Making the modeling approaches developed in Rosetta available to the wide community of molecular biologists, with varying proficiencies in programming, demands a framework that does not suffer from the rigidities of traditional programming languages
With these goals in mind, we developed RosettaScripts, an XMLlike language for specifying modeling protocols in the Rosetta framework

Summary

Introduction

The Rosetta software suite for macromolecular modeling has useful applications in many areas of interest to molecular biologists. RosettaScripts provides protocol-level access to modeling functionalities, such as loop modeling, rigid-body docking, and sequence design. A RosettaScript consists of five tags, each of which contains subtags: MOVERS, FILTERS, SCOREFXNS, TASKOPERATIONS, and PROTOCOLS (Fig. 1A).

Results

Conclusion