title: A Framework to Simplify Combined Sampling Strategies in Rosetta.
abstract: A core task in computational structural biology is the search of conformational space for low energy configurations of a biological macromolecule. Because conformational space has a very high dimensionality, the most successful search methods integrate some form of prior knowledge into a general sampling algorithm to reduce the effective dimensionality. However, integrating multiple types of constraints can be challenging. To streamline the incorporation of diverse constraints, we developed the Broker: an extension of the Rosetta macromolecular modeling suite that can express a wide range of protocols using constraints by combining small, independent modules, each of which implements a different set of constraints. We demonstrate expressiveness of the Broker through several code vignettes. The framework enables rapid protocol development in both biomolecular design and structural modeling tasks and thus is an important step towards exposing the rich functionality of Rosetta's core libraries to a growing community of users addressing a diverse set of tasks in computational biology.
authors.affiliation: School of Medicine, Washington University in St. Louis, Missouri, Washington, United States of America.
authors.forename: Justin R
authors.initials: JR
authors.lastname: Porter
authors.affiliation: Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America.
authors.forename: Brian D
authors.initials: BD
authors.lastname: Weitzner
authors.affiliation: Lehrstuhl für Biomolekulare NMR-Spektroskopie, Fakultät Chemie, Techniche Universität München, Munich, Germany.
authors.forename: Oliver F
authors.initials: OF
authors.lastname: Lange
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D046911:Macromolecular Substances / Q000737:chemistry / Q000378:metabolism; D008958:Models, Molecular; D062105:Molecular Docking Simulation; D011485:Protein Binding; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry / Q000378:metabolism; D012984:Software
chemical_list: D046911:Macromolecular Substances; D011506:Proteins