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Título

A reverse combination of structure-based and ligand-based strategies for virtual screening

Autor Cortés Cabrera, Álvaro; Gago, Federico ; Morreale, Antonio
Palabras clave Fragment screening
Structure-based virtual screening
Ligand-based virtual screening
Docking
Drug design
Fecha de publicación 2012
EditorKluwer Academic Publishers
Citación Journal of Computer-Aided Molecular Design 26: 319- 327 (2012)
ResumenA new approach is presented that combines structure- and ligand-based virtual screening in a reverse way. Opposite to the majority of the methods, a docking protocol is first employed to prioritize small ligands (>fragments>) that are subsequently used as queries to search for similar larger ligands in a database. For a given chemical library, a three-step strategy is followed consisting of (1) contraction into a representative, non-redundant, set of fragments, (2) selection of the three best-scoring fragments docking into a given macromolecular target site, and (3) expansion of the fragments' structures back into ligands by using them as queries to search the library by means of fingerprint descriptions and similarity criteria. We tested the performance of this approach on a collection of fragments and ligands found in the ZINC database and the directory of useful decoys, and compared the results with those obtained using a standard docking protocol. The new method provided better overall results and was several times faster. We also studied the chemical diversity that both methods cover using an in-house compound library and concluded that the novel approach performs similarly but at a much smaller computational cost. © Springer Science+Business Media B.V. 2012.
URI http://hdl.handle.net/10261/111515
DOI10.1007/s10822-012-9558-x
Identificadoresdoi: 10.1007/s10822-012-9558-x
issn: 0920-654X
Aparece en las colecciones: (CBM) Comunicaciones congresos
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