Int. J. Mol. Sci. 2007, 8(11), 1083-1094; doi:10.3390/i8111083
Article

A Fragment-Based Scoring Function to Re-rank ATP Docking Results

1 M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul. Miklukho-Maklaya, 16/10, 117997 GSP, Moscow V-437, Russia 2 Moscow Institute of Physics and Technology (State University), 141700, Institutskii per., 9, Dolgoprudny, Moscow region, Russia
* Author to whom correspondence should be addressed.
Received: 3 August 2007; in revised form: 29 September 2007 / Accepted: 22 October 2007 / Published: 31 October 2007
(This article belongs to the Section Molecular Recognition)
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Abstract: ATP is involved in numerous biochemical reactions in living cells interacting withdifferent proteins. Molecular docking simulations provide considerable insight into theproblem of molecular recognition of this substrate. To improve the selection of correctATP poses among those generated by docking algorithms we propose a post-docking rerankingcriterion. The method is based on detailed analysis of the intermolecularinteractions in 50 high-resolution 3D-structures of ATP-protein complexes. A distinctivenew feature of the proposed method is that the ligand molecule is divided into fragmentsthat differ in their physical properties. The placement of each of them into the bindingsite is judged separately by different criteria, thus avoiding undesirable averaging of thescoring function terms by highlighting those relevant for particular fragments. Thescoring performance of the new criteria was tested with the docking solutions for ATPproteincomplexes and a significant improvement in the selection of correct dockingposes was observed, as compared to the standard scoring function.
Keywords: ATP recognition; molecular hydrophobicity potential; molecular lipophilicity; potential; stacking

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MDPI and ACS Style

Pyrkov, T.V.; Efremov, R.G. A Fragment-Based Scoring Function to Re-rank ATP Docking Results. Int. J. Mol. Sci. 2007, 8, 1083-1094.

AMA Style

Pyrkov TV, Efremov RG. A Fragment-Based Scoring Function to Re-rank ATP Docking Results. International Journal of Molecular Sciences. 2007; 8(11):1083-1094.

Chicago/Turabian Style

Pyrkov, Timothy V.; Efremov, Roman G. 2007. "A Fragment-Based Scoring Function to Re-rank ATP Docking Results." Int. J. Mol. Sci. 8, no. 11: 1083-1094.

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