Title:
Binding Balls: Fast Detection of Binding Sites Using a Property of Spherical Fourier Transform
Binding Balls: Fast Detection of Binding Sites Using a Property of Spherical Fourier Transform
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Author(s)
Comin, Matteo
Guerra, Concettina
Dellaert, Frank
Guerra, Concettina
Dellaert, Frank
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Abstract
The functional prediction of proteins is one of the most challenging problems in modern
biology. An established computational technique involves the identification of threedimensional
local similarities in proteins. In this article, we present a novel method to
quickly identify promising binding sites. Our aim is to efficiently detect putative binding
sites without explicitly aligning them. Using the theory of Spherical Harmonics, a candidate
binding site is modeled as a Binding Ball. The Binding Ball signature, offered by the
Spherical Fourier coefficients, can be efficiently used for a fast detection of putative regions.
Our contribution includes the Binding Ball modeling and the definition of a scoring function
that does not require aligning candidate regions. Our scoring function can be computed
efficiently using a property of Spherical Fourier transform (SFT) that avoids the evaluation
of all alignments. Experiments on different ligands show good discrimination power when
searching for known binding sites. Moreover, we prove that this method can save up to 40%
in time compared with traditional approaches.
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Date Issued
2009
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Text
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Article