A framework to simplify combined sampling modes in Rosetta

PLOS ONE, 2015: https://doi.org/10.1371/journal.pone.0138220

Suggested citation: Porter JR, Weitzner BD, Lange OF (2015) “A framework to simplify combined sampling modes in Rosetta,” PLOS ONE 10(9): e0138220. DOI: 10.1371/journal.pone.0138220

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.