. Author manuscript; available in PMC: 2011 Jul 1.

Published in final edited form as: Proteins. 2010 Jul;78(9):2007–2028. doi: 10.1002/prot.22715

Table 9.

Running speed of the programs.

Phase	Task	Duration (seconds)
Preparation	Extracting a pocket (by LIGSITE)	4.3

	p-Z moments: Projecting the pocket with ray-tracing	9.1
	3DZD: surface voxelization	24.0

	p-Z moments: Computing the pseudo-Zernike moments	1.1
	3DZD: Computing 3DZD	16

Database Search	Computing the distance against pockets in the database p-Z moments:	0.0075
	3DZD:	0.018

	Sorting and scoring p-Z moments:	0.005
	3DZD:	0.005

The speed of each task is the average of 5 executions on a Linux machine with a Pentium 4, 3.0GHz processor. The protein PDB entry 1h2h is scanned by LIGSITE to identify its largest pocket. Then the p-Z moments and the 3DZD for the largest pocket is computed. The database scanned is the same as used in the benchmark of this study (i.e. the 100 pockets).