Abstract
The examination and analysis of super-secondary structures or other specific structural patterns associated with particular functions, sequence motifs, or structural contexts require that the set of structures examined shares the same feature. This seems obvious but in practice this may often present problems such as identifying complete sets of data avoiding false positives. In the case of the β-propeller structures the symmetry of the propeller creates problems for many structure similarity search programs. Here we present a procedure that will identify propeller structures in PDB and assign them to the different N-propeller types. In addition we outline methods to examine similarities and differences within and between the four stranded up-and-down blades of the β-propeller.
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Acknowledgments
We wish to thank The Lundbeck Foundation for financial support through the MIND Centre and The Danish National Research Foundation for funding through the CARB Centre.
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Thirup, S., Gupta, V., Quistgaard, E.M. (2012). Up, Down, and Around: Identifying Recurrent Interactions Within and Between Super-secondary Structures in β-Propellers. In: Kister, A. (eds) Protein Supersecondary Structures. Methods in Molecular Biology, vol 932. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-065-6_3
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DOI: https://doi.org/10.1007/978-1-62703-065-6_3
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