%0 Journal Article
%T Multipolar representation of protein structure
%A Apostol Gramada
%A Philip E Bourne
%J BMC Bioinformatics
%D 2006
%I BioMed Central
%R 10.1186/1471-2105-7-242
%X Here we propose such a parameterization and study its relationship to the standard Euclidian description based on amino acid representative coordinates. The representation uses multipoles associated with residue C¦Á coordinates as shape descriptors. We demonstrate that the multipoles can be used for the quantitative description of the protein shape and for the comparison of protein structures at various levels of detail. Specifically, we construct a (dis)similarity measure in multipolar configuration space, and show how such a function can be used for the comparison of a pair of proteins. We then test the parameterization on a benchmark set of the protein kinase-like superfamily. We prove that, when the biologically relevant portions of the proteins are retained, it can robustly discriminate between the various families in the set in a way not possible through sequence or conventional structural representations alone. We then compare our representation with the Cartesian coordinate description and show that, as expected, the correlation with that representation increases as the level of detail, measured by the highest rank of multipoles used in the representation, approaches the dimensionality of the fold space.The results described here demonstrate how a granular description of the protein structure can be achieved using multipolar coefficients. The description has the additional advantage of being immediately generalizable for any residue-specific property therefore providing a unitary framework for the study and comparison of the spatial profile of various protein properties.The functions of a protein are determined by its three dimensional structure. It is believed that the functional space of all proteins can be spanned by combining a rather small number of structural units, termed folds. The number of different folds is small compared to the total number of proteins, of the order of 1000 for globular, water-soluble proteins [1]. This is in contrast with the exp
%U http://www.biomedcentral.com/1471-2105/7/242