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Article ID: 129 - Last Modified: December 4, 2010

Does Phase report the best or the first alignment in the Project Table, after screening a database with a hypothesis?

By default, hits are sorted globally from compound to compound, so the hits at the top of the Project Table have the highest fitness. And if you limit the total number of hits returned to, say, 1000, you get the best 1000.

There's a slight exception to this rule, however, if you request more than one hit per compound. In that case, the hits for a given compound are grouped and sorted by fitness, and the overall hit list is sorted by the fitness of the top-ranked hit for each compound. So if you request a maximum of 3 hits per compound, you might see a hit list like the following, where '*' indicates the values on which the groups of hits are sorted:

Compound Fitness
mol_2358 2.89751*
mol_2358 2.78443
mol_2358 2.60250
mol_112 2.85592*
mol_112 2.80317
mol_112 2.54346
mol_5733 2.82459*
mol_5733 2.72332
mol_5733 2.61260
etc.

So if you limit the number of hits to 1000, only a few hundred compounds will be represented, and you won't get the absolute best 1000 hits. But you will get the best hits for each compound that appears in the list.

Keywords: Phase, pharmacophore, hypothesis, find matches, fitness score, Maestro

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