Publications

A deterministic algorithm for constrained enumeration of transmembrane protein folds

Faulon, Jean-Loup M.; Sale, Kenneth L.; Schoeniger, Joseph S.; Young, Malin M.

A deterministic algorithm for enumeration of transmembrane protein folds is presented. Using a set of sparse pairwise atomic distance constraints (such as those obtained from chemical cross-linking, FRET, or dipolar EPR experiments), the algorithm performs an exhaustive search of secondary structure element packing conformations distributed throughout the entire conformational space. The end result is a set of distinct protein conformations, which can be scored and refined as part of a process designed for computational elucidation of transmembrane protein structures.