CombiDOCK

OptiDOCK An extension of the CombiDOCK methodology, which selects a diverse but representative subset of compounds that span the structural space encompassed by the full library Tripos, Inc. http //www.tripos.com [33]... 

Fig. 8.1. Schematic depiction of the seed and grow docking approach for structure-based library design. The programs that use this approach include CombiDOCK and PR0 SELECT.

CombiDock Tweaks the DOCK algorithm to identify suitable scaffold orientations in the binding pocket. Proceeds using the seed and grow approach to design combinatorial libraries (73)... 

I. D. (1998) CombiDOCK structure-based combinatorial docking and library design. J Comput Aided Mol Des 12, 597-604. 

CombiDOCK Structure-Based Combinatorial Docking and Library Design. 

The combinatorial docking tools PRO SELECT [121] and CombiDOCK [122] are based on the incremental construction method. In both approaches, a library is formed by a template (or core) molecule with a set of attachment points to which one out of a predefined set of substituents can be connected. The template is then positioned in the active site without considering the substituents. Starting from a few orientations of the template, the substituents are placed into the active site of the protein independently. In case of PRO SELECT, substituents are then selected based on score and additional criteria like 2D similarity and feasibility of synthesis. CombiDOCK calculates a final score for whole library molecules by combining fragment scores. 

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