Available Tools and Protocols

Of the de novo design papers published to date, only a few provide details of tools or procedures used to help cope with large numbers of generated structures. In this section, each of these is described. 

The work reported by Eisen et describes a specialized analysis tool called TABLE. To set the context for our discussion of the TABLE functionality, we give a short description of the HOOK program. 

TABLE analyzes that output file and allows interactive manipulation of the data generated by the HOOK program by means of spreadsheet-like functions. These capabilities allow a user of HOOK to select molecules from a larger set by setting various criteria of significance to the user. TABLE also acts 

A further illustration of the use of the TABLE functions was given recently by Caflisch and Karplus, who sorted 4494 potential thrombin ligands by the number of hooked groups and overlap score. According to Eisen et al., the flexibility of the TABLE program allows other methods of ranking the structures from the HOOK program to be incorporated easily. 

As mentioned in the introduction to this section, Bohacek and McMar-tin generated a set of 22,000 structures in the active site of thermolysin using their GrowMol program. The procedure they adopted for identifying the most promising of these structures was disclosed in detail and can be summarized as follows. 

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