Titel
Greedy 3-Point Search (G3PS)—A Novel Algorithm for Pharmacophore Alignment
Abstract
Chemical features of small molecules can be abstracted to 3D pharmacophore models, which are easy to generate, interpret, and adapt by medicinal chemists. Three-dimensional pharmacophores can be used to efficiently match and align molecules according to their chemical feature pattern, which facilitates the virtual screening of even large compound databases. Existing alignment methods, used in computational drug discovery and bio-activity prediction, are often not suitable for finding matches between pharmacophores accurately as they purely aim to minimize RMSD or maximize volume overlap, when the actual goal is to match as many features as possible within the positional tolerances of the pharmacophore features. As a consequence, the obtained alignment results are often suboptimal in terms of the number of geometrically matched feature pairs, which increases the false-negative rate, thus negatively affecting the outcome of virtual screening experiments. We addressed this issue by introducing a new alignment algorithm, Greedy 3-Point Search (G3PS), which aims at finding optimal alignments by using a matching-feature-pair maximizing search strategy while at the same time being faster than competing methods.
Stichwort
pharmacophore alignmentpharmacophore modellingvirtual screeninggreedy algorithmdrug design
Objekt-Typ
Sprache
Englisch [eng]
Persistent identifier
https://phaidra.univie.ac.at/o:1588272
Erschienen in
Titel
Molecules
Band
26
Ausgabe
23
ISSN
1420-3049
Erscheinungsdatum
2021
Verlag
MDPI AG
Erscheinungsdatum
2021
Zugänglichkeit
Rechteangabe
© 2021 by the authors

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