Book of Abstracts: Albany 2003
June 17-21 2003
Towards the Prediction of Novel DNA-binding Protein Structures
It has been estimated that 6-7% of the proteins of Eukaryotic genomes are DNA binding proteins and while many different families have been detected it is likely that a number of novel DNA structures will be found from Structural Genomics Initiatives. Given the electric charge distribution within DNA (and in particular the negative charged region around the base pairs), it seems plausible to look for structures with a significant regions of posative electrostatic potential on its surface. For each surface atom of a protein, we can construct a score proportional to the surface integral of the electrostatic potential (computed using Delphi) in the neighbourhood of the atom and construct a simple patch score, rather than using the potential at a discrete number of points. We employ a set of DNA binding proteins as a test set to examine the accuracy of this approach.
European Bioinformatics Institute
Wellcome Trust Genome Campus