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.

SUBMITTER: Porter JR 

PROVIDER: S-EPMC4575156 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature