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Next: Alignment of structure-mapped sequence Up: Mapping of structure and Previous: Sequence conservation   Contents

Predicted secondary structure information

The architectures of proteins show, to a certain extent, a tendency for the two main secondary structure types to form layers and or local clusters. $\beta $-sheets clearly form layers, but in many mixed-$\alpha \beta $ class proteins, helices form parallel layers on one or two sides of the sheet (see the $\alpha \beta $ sandwich architectures in CATH). In the case of $\alpha \beta $ barrels, the strands form the core, whilst helices lie on the exterior.

The mapping of experimentally determined secondary structure information would not have any use in prediction. However the mapping of secondary structure prediction probabilities with three-dimensional coordinates has the potential to `smooth out' errors. This cannot be used to improve the predictions themselves, of course, but has a possible application in fold recognition. No mappings are shown for secondary structure information.



Copyright Bob MacCallum - DISCLAIMER: this was written in 1997 and may contain out-of-date information.