Mapping of physicochemical features onto surfaces of biomolecules can provide valuable insight into their function. Such information can be used to characterize and identify similarities in the surface regions of proteins. Surface Diver quantitatively describes various physicochemical properties such as hydrophobicity, charge density, and electrostatic potential of a biomolecule, using a method based on 3D Spherical Harmonic Decomposition. The method introduces a compact representation of a given property defined on the surface of the molecule using a finite set of rotation-invariant descriptors. Rotation-invariance of these descriptors allows one to compare proteins with respect to their shape and physicochemical properties without the need for any prior structural alignement.

 

If you find Surface Diver useful, please acknowledge its use by citing:

Maciej Dlugosz, Joanna Trylska Electrostatic similarity of proteins: Application of 3D spherical harmonic decomposition, J. Chem. Phys., 129:015103, 2008

 

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