Designed by N. Sukumar, Jeffrey G. Martin and Curt M. Breneman
© Rensselaer Polytechnic Institute, 2001-2006

Since the DNA structure is, to a first approximation, fairly rigid, and the most important sequence-specific interactions between proteins and DNA are often in the major groove, we represent electron density features such as electrostatic potential (EP) and local average ionization potential (PIP) on the accessible surfaces of the major groove, on a grid of rectangles (the "Dixel" coordinate system) where each base pair is represented by 10 surface pixels of size 1.6 Angstroms (along the base pair) by 3.4 Angstroms (parallel to the axis of the DNA helix). These generate an abstract representation of chemical features of the accessible surface of the DNA major groove using TAE properties for base pairs in their native electronic environments.

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