Hit clustering can improve virtual fragment screening ... - Springer Link
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Hit clustering can improve virtual fragment screening ... - Springer Link
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ORIGINAL PAPER
Hit clustering can improve virtual fragment screening: CDK2 and PARP1 case studies Alexey A. Zeifman & Victor S. Stroylov & Fedor N. Novikov & Oleg V. Stroganov & Alexandra L. Zakharenko & Svetlana N. Khodyreva & Olga I. Lavrik & Ghermes G. Chilov
Received: 12 May 2011 / Accepted: 12 October 2011 / Published online: 9 November 2011 # Springer-Verlag 2011
Abstract Virtual fragment screening could be a promising alternative to existing experimental screening techniques. However, reliable methods of in silico fragment screening are yet to be established and validated. In order to develop such an approach we first checked how successful the existing molecular docking methods can be in predicting fragment binding affinities and poses. Using our Lead Finder docking software the RMSD of the binding energy prediction was observed to be 1.35 kcal/mol−1 on a set of 26 experimentally characterized fragment inhibitors, and the RMSD of the predicted binding pose from the experimental one was
