A deterministic algorithm for constrained enumeration of transmembrane protein folds.
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.
Brown
W Michael
WM
Computational Biology, Sandia National Laboratories, Albuquerque, NM 87123, USA. wmbrown@sandia.gov
Faulon
Jean-Loup
JL
Sale
Ken
K
D000465:Algorithms; D002462:Cell Membrane / Q000737:chemistry; D003432:Cross-Linking Reagents / Q000737:chemistry; D004578:Electron Spin Resonance Spectroscopy; D031541:Fluorescence Resonance Energy Transfer; D008565:Membrane Proteins / Q000737:chemistry*; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary
D003432:Cross-Linking Reagents; D008565:Membrane Proteins