Table 2. Program Comparisons^a.

program	average volume ± SD	run time (1 thread)	run time (24 threads)
POVME 1.0		10500
POVME 2.0	2071.3 ± 129.1	16	2
POVME 2.0/convex hull	1021.8 ± 154.8	92	8
trj_cavity	814.4 ± 254.6	16
MDpocket	523.2 ± 60.5	11
PocketAnalyzerPCA	811.5 ± 100.2	96*
EPOSBP without clustering		43
EPOSBP with clustering		259

^aThe average pocket volume (in ų), plus or minus the standard deviation, measured over the course of a REL1 trajectory using several pocket-analysis programs. Note that the POVME 1.0 results were, for all intents and purposes, identical to the POVME 2.0 results with the convex-hull feature disabled. Additionally, EPOS^BP volume measurements are not included because that program does not output volume-per-frame data. The total run times for each program are given in minutes. A PCA calculation accounted for approximately 6 min of the PocketAnalyzer^PCA run time (marked with an asterisk). As POVME 2.0 is designed to use multiple processors, the run times for parallel POVME 2.0 calculations are also shown.