fPOP: Footprinting protein functional
surfaces by comparative
spatial patterns
by Yan Yuan Tseng, Jeffrey Chen, and Wen-Hsiung Li.
University of Chicago
fPOP (footprinting Pockets Of Proteins, http://pocket.med.wayne.edu/fpop/)
is a database of the protein functional surfaces identified by shape
analysis. In this relational database, we collected the spatial patterns
of protein binding sites including both holo and apo forms from more than
40,000 structures. To identify protein binding sites, we model the shape
of a split pocket induced by a binding ligand(s). Essentially, we use
a purely geometric method to extract site-specific spatial patterns of
split pockets as templates to match those from unbound structures. To
perform an effective shape comparison, we utilize the Smith-Waterman
algorithm to footprint an unbound pocket fragment with those selected from the
canonical functional surfaces of >19,000 structures in the SplitPocket
(http://pocket.med.wayne.edu/). The pairwise alignment of the unbound and
split-pocket fragments is superimposed to evaluate the local structural
similarity for detecting the unbound split characteristic through the
RMSD measurement. Furthermore, we conduct a large-scale computation to
systematically identify binding sites of proteins. In addition to the
geometric measurements, we extensively measure the propensity of surface
conservation encapsulated in the evolutionary history.(more)
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