A deterministic algorithm for enumeration of transmembrane protein folds is implemented. 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. Algorithm Overview: The ESSEB algorithm works by dividing the conforrnational space of each secondary structure element (SSE) into a set of cells. For each cell there is a representative conformation and for each atom in the SSE for which a distance restraint is available, there is an associated internal error, The internal error for a distance restraint is the maximum distance that the atom, when positioned in any conformation within a cell, can be from the atom in the representative conformation. The algorithm works recursively by positioning one representative conformation of an SSE. AdI distance restraints are checked with a tolerance that includes both the experimental and internal error. If all restraints are satisfied, every representative conformation of the next SSE is checked, otherwise, the program moves on to the next representative conformation of the current SSE. In addition to the distance restraints, other constraints on protein conformation can be enforced. These include the distance of closest approach between SSE axes, a restraint which prevents the crossover of loops connecting adjacent SSEs, and a restriction on the minimum and maximum distances between axis end-points. Any protein conformation satisfying all of the restraints is enumerated for later scoring and possible refinement. Additionally, in order to make run-times feasible, a divide-and-conquer approach is used in which the cells of each SSE in an accepted protein conformation can be further divided such that the internal errors are reduced and the new representative conformations can be evaluated.
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@misc{osti_1230783,
title = {Enumeration of Secondary Structure Element Bundles, Version 00},
author = {Brown, William Michael and Faulon, Jean-Loup},
abstractNote = {A deterministic algorithm for enumeration of transmembrane protein folds is implemented. 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. Algorithm Overview: The ESSEB algorithm works by dividing the conforrnational space of each secondary structure element (SSE) into a set of cells. For each cell there is a representative conformation and for each atom in the SSE for which a distance restraint is available, there is an associated internal error, The internal error for a distance restraint is the maximum distance that the atom, when positioned in any conformation within a cell, can be from the atom in the representative conformation. The algorithm works recursively by positioning one representative conformation of an SSE. AdI distance restraints are checked with a tolerance that includes both the experimental and internal error. If all restraints are satisfied, every representative conformation of the next SSE is checked, otherwise, the program moves on to the next representative conformation of the current SSE. In addition to the distance restraints, other constraints on protein conformation can be enforced. These include the distance of closest approach between SSE axes, a restraint which prevents the crossover of loops connecting adjacent SSEs, and a restriction on the minimum and maximum distances between axis end-points. Any protein conformation satisfying all of the restraints is enumerated for later scoring and possible refinement. Additionally, in order to make run-times feasible, a divide-and-conquer approach is used in which the cells of each SSE in an accepted protein conformation can be further divided such that the internal errors are reduced and the new representative conformations can be evaluated.},
doi = {},
url = {https://www.osti.gov/biblio/1230783},
year = {Tue Oct 26 00:00:00 EDT 2004},
month = {Tue Oct 26 00:00:00 EDT 2004},
note =
}
