 
Summary: The ContourBuildup Algorithm to Calculate the Analytical
Molecular Surface
MAXIM TOTROV
Skirball Institute of Biomolecular Medicine, NYU Medical Center, 540 First Avenue, New York, New York 10016
AND
RUBEN ABAGYAN
Department of Biochemistry and Skirball Institute of Biomolecular Medicine, NYU Medical Center,
Courant Institute of Mathematics, 540 First Avenue, New York, New York 10016
Received October 1, 1995, and in revised form October 19, 1995
A new algorithm is presented to calculate the an
alytical molecular surface defined as a smooth en
velope traced out by the surface of a probe sphere
rolled over the molecule. The core of the algorithm
is the sequential build up of multiarc contours on
the van der Waals spheres. This algorithm yields
substantial reduction in both memory and time re
quirements of surface calculations. Further, the
contourbuildup principle is intrinsically ``local'',
which makes calculations of the partial molecular
surfaces even more efficient. Additionally, the algo
