Geometric molecular surface modeling using mathematical morphology operators. Journal of Molecular Graphics Volume 13, Issue 6, Pages 331-388 (December.

Geometric molecular surface modeling using

mathematical morphology operators.

Journal of Molecular Graphics Volume 13, Issue 6, Pages 331-388 (December 1995) : 331-336. Masato Masuya and Junta Doi

Ri - atom radius

van der Waals surface Sv and its interior Iv:

Rw - probe radius

Solvent Accessible surface and its interior:

Molecular surface and its interior:

Cavity and Convex Portion Detection

Cf = SIm ● R

Remove small cavities smaller than a water molecule (Rw):

Cf filled molecule

( )f cmC C SI

Cavities:

Pr = SIm ○ R

( )r cmP SI P

Remove small convex parts (Rw):