Table 3.

An overview and availability of a few surface-based shape comparison methods.

Method	Description	Availability	References
SURFCOMP	Molecular surface is divided into patches and corresponding patches are identified using geometrically invariant descriptors and physicochemical properties.	Available on request.	Hofbauer et al., 2004
ParaFit	Performs 3D superposition and surface property comparison. Electronic surface properties are calculated using ParaSurf program. Spherical harmonics expansion coefficients of molecular surface are used.	Developed by CEPOS in silico Ltd. Commercial or Academic license can be obtained at http://www.ceposinsilico.de/	Mavridis et al., 2007
SHeMS	Uses spherical harmonics description of shape. Weights of spherical harmonics expansion coefficients are optimized using a genetic algorithm.	Developed by Shanghai Key Laboratory of New Drug Design, East China University of Science & Technology, Shanghai, China. Obtained by contacting Prof. Honglin Li at http://lilab.ecust.edu.cn/home/resource.html	Cai et al., 2012
HPCC	Combined spherical harmonics shape comparison with pharmacophoric features. Tanimoto similarity coefficients for shape and chemical similarity are added to evaluate similarity between two molecules.	Developed by Harmonic Pharma. May be available from https://www.harmonicpharma.com/oncology/	Karaboga et al., 2013
3DZD	Uses 3D Zernike descriptors which are extension of spherical harmonics. Rotation translation invariant.	Developed by Kihara Bioinformatics laboratory at Purdue University, USA. Several implementations of 3DZD are available either as standalone program or web-server at http://kiharalab.org/contact.php	Sael et al., 2008a, Venkatraman et al., 2009a