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Article ID: 203 - Last Modified: December 4, 2010

How long does it take to screen a Phase database?

Screening time is dependent on a number of factors, so we cannot give an number of hours to do a screen. It depends on the speed of the disk, the number of processors, and most importantly, the nature of the query. A highly selective hypothesis that matches only a small fraction of compounds will result in a much faster search. In our experience, a screen that matches only about 5% of the database will proceed at a speed of about 25 compounds per second per processor. That takes into account the fact that most compounds will be eliminated in the key-based pre-screen, so each processor is not actually searching 25 compounds per second. Rather, 25 compounds/sec is the formal speed based on the number of compounds formally assigned to each of the N subjobs = 3.1e06/N. If N = 10, such a screen is going to take about 4 hours, assuming no significant lag in queuing subjobs, and no differences in processor speeds. But a search could take much longer if the hypothesis is very generic, or if partial matching is used.

Keywords: Phase, database screening, speed

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