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Article ID: 1121 - Last Modified: March 29, 2011

Following a protocore docking run, which file contains the results?

The output of Alignment is the jobname_dressed_lib.mae file. This file contains the new scaffolds with the side chains of the template molecule attached. The structures are sorted in order of number of attachments that could be matched (descending) and then by goodness of alignment (ascending RMS). For Alignment-only jobs, this is the file that should be examined. If redocking of the aligned structures has been done, the output of this stage, jobname_lib.mae, should be examined. Its structures are sorted by GlideScore, in ascending order.

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