Novel DOCK clique driven 3D similarity database search tools for molecule shape matching and beyond: adding flexibility to the search for ligand kin.

Novel DOCK clique driven 3D similarity database search tools for molecule shape matching and beyond: adding flexibility to the search for ligand kin. Research Abstract Details 

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Novel DOCK clique driven 3D similarity database search tools for molecule shape matching and beyond: adding flexibility to the search for ligand kin. Abstract Text:

Andrew C Good,Andrew C Good,

With readily available CPU power and copious disk storage, it is now possible to undertake rapid comparison of 3D properties derived from explicit ligand overlay experiments. With this in mind, shape software tools originally devised in the 1990s are revisited, modified and applied to the problem of ligand database shape comparison. The utility of Connolly surface data is highlighted using the program MAKESITE, which leverages surface normal data to a create ligand shape cast. This cast is applied directly within DOCK, allowing the program to be used unmodified as a shape searching tool. In addition, DOCK has undergone multiple modifications to create a dedicated ligand shape comparison tool KIN. Scoring has been altered to incorporate the original incarnation of Gaussian function derived shape description based on STO-3G atomic electron density. In addition, a tabu-like search refinement has been added to increase search speed by removing redundant starting orientations produced during clique matching. The ability to use exclusion regions, again based on Gaussian shape overlap, has also been integrated into the scoring function. The use of both DOCK with MAKESITE and KIN in database screening mode is illustrated using a published ligand shape virtual screening template. The advantages of using a clique-driven search paradigm are highlighted, including shape optimization within a pharmacophore constrained framework, and easy incorporation of additional scoring function modifications. The potential for further development of such methods is also discussed.

Novel DOCK clique driven 3D similarity database search tools for molecule shape matching and beyond: adding flexibility to the search for ligand kin. Publishing Authors By Initials

AC Good,AC Good,

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Novel DOCK clique driven 3D similarity database search tools for molecule shape matching and beyond: adding flexibility to the search for ligand kin. Journal Published:

PUBLICATION TYPE: Journal Article

Journal: Journal of molecular graphics & modelling

VOLUME: 26

Page Numbers: 656-66

Journal Abbreviation: J. Mol. Graph. Model.

ISSN: 1093-3263

DAY: 4

MONTH: 04

YEAR: 2007

Novel DOCK clique driven 3D similarity database search tools for molecule shape matching and beyond: adding flexibility to the search for ligand kin. Information

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LANGUAGE: eng

NlmUniqueID: 9716237

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Grant and Affiliation Information for Novel DOCK clique driven 3D similarity database search tools for molecule shape matching and beyond: adding flexibility to the search for ligand kin.

AFFILIATION: Bristol-Myers Squibb, PO Box 5100, Wallingford, CT 06492, USA. andrew.good@bms.com

Country: United States

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MEDLINETA: J Mol Graph Model

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