[talks] T Capra preFPO

Melissa Lawson mml at CS.Princeton.EDU
Wed Oct 29 13:59:45 EDT 2008

Tony Capra will present his preFPO on Monday November 3 at 1PM in Room 401 (note room). 
The members of his committee are:  Mona Singh, advisor; Tom Funkhouser and Olga
readers; Fred Hughson (MOL) and Chris Floudas (CHE), nonreaders.  Everyone is invited to
his talk.  His abstract follows below.

Predicting functionally important residues in proteins from evolutionary conservation and
3D structure

All residues in a protein are not equally important.  Some are essential to maintain the
proper structure and function of the protein, while others tolerate replacement by
different amino acids.  Identifying the functionally important sites in a protein is an
important step towards characterizing its molecular function and has direct applications
to drug design and protein engineering.  In this talk, I will describe three projects that
substantially improve our understanding of and ability to predict functionally important

First, I will present an information theoretic algorithm for predicting functionally
important sites using evolutionary conservation. It acheives state-of-the-art performance
and is several orders of magnitude faster than other competitive approaches.

I will then describe a bioinformatics pipeline we developed to create the first large
dataset of specificity determining positions (SDP). This dataset allows us to characterize
properties of SDP and demonstrate that existing SDP prediction methods do not perform as
well as a simple approach we developed.

Last, I will introduce a method that combines our new conservation-based measure with 3D
models of protein structures to signficantly improve the identification of ligand-binding

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