What's New in DOCK 4.0

Table 1. New Features

Orientation Search

The binding mode orientation search of dock has been rewritten, so that matching is now completely exhaustive within the geometric bounds specified by the user. The orientation search can be performed in several ways, as Automated Matching , as Manual Matching , or as a Random Search .

Conformation Search

All rotatable bonds are searched exhaustively using the Simultaneous Search . Alternatively, a rigid core is docked and the flexible parts reattached incrementally using the Anchor-First Search . Conformations are locally optimized.

Chemical Score

Chemical complementarity of docked molecules may be enhanced with a user-tailored scoring function. The "chemical score" may be partitioned into any number of chemical interactions whose definitions are under complete user control.

Chemical Screen

Molecules may be rapidly filtered with a Similarity Screen based on an active molecule or with a Pharmacophore Screen .

Dock Functionality

Docking functions have been separated into independent components. Each may be combined in a flexible fashion to perform many different computational tasks.

 

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