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Locating a binding pocket

This is a quick tutorial to indicate a trick that sometimes works for finding binding pockets and other deep cavities in protein surfaces. Start spock and type

fetch=1brl.pdb; makesurf

to load bacterial luciferase and surface it, or you can accomplish the same tasks with the menus. Notice that this surface is quite complicated, and finding something on it might be difficult. On the ``Alter tex2html_wrap_inline6800 Surfaces'' menu, toggle ``Reduce when building'' to on, and select ``Resmooth surface''. Enter 5 times for the smoothing. Spock will smooth and simplify the molecular surface, so that important surface features are easier to spot. Depending on the initial complexity of other surfaces, you may have to smooth them more or less times to get the right level of detail.

Jon Christopher
Tue Sep 14 16:44:48 CDT 1999