A deterministic algorithm for constrained enumeration of transmembrane protein folds

  • Authors:

  • W. Michael Brown;Jean-Loup Faulon;Ken Sale

  • Affiliations:

  • Computational Biology, Sandia National Laboratories, Albuquerque, NM 87123, USA;Computational Biology, Sandia National Laboratories, Albuquerque, NM 87123, USA;Biosystems Research Department, Sandia National Laboratories, Livermore, CA 94551, USA

  • Venue:
  • Computational Biology and Chemistry
  • Year:
  • 2005

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Abstract

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.