Tuning interval Branch-and-Prune for protein structure determination

The interval Branch and Prune ( i BP) algorithm for obtaining solutions to the interval Discretizable Molecular Distance Geometry Problem ( i DMDGP) has proven itself as a powerful method for molecular structure determination. However, substantial obstacles still must be overcome before i BP may be employed as a tractable general-purpose alternative to existing structure determination algorithms. This work introduces an iterative variant of the i BP algorithm that leverages existing knowledge of protein structures in order to reduce the size of the effective search space by many orders of magnitude. These improvements are included in a newly released implementation of the i BP software that aims to provide a solid platform for both research and application of the i DMDGP.