A deterministic algorithm for constrained enumeration of transmembrane protein folds.

W Michael Brown; Jean-Loup Faulon; Ken Sale

doi:10.1016/j.compbiolchem.2005.03.001

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A deterministic algorithm for constrained enumeration of transmembrane protein folds.

W Michael Brown·Jean-Loup Faulon·Ken Sale

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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.

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Algorithms Cell Membrane Cross-Linking Reagents Electron Spin Resonance Spectroscopy Fluorescence Resonance Energy Transfer Membrane Proteins Protein Folding Protein Structure, Secondary Protein Structure, Tertiary Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

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W Michael Brown, Jean-Loup Faulon, Ken Sale. 2005. A deterministic algorithm for constrained enumeration of transmembrane protein folds.. https://doi.org/10.1016/j.compbiolchem.2005.03.001

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