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Pharmacophore alignment search tool: Influence of canonical atom labeling on similarity searching.
Hähnke, Volker; Rupp, Matthias; Krier, Mireille; Rippmann, Friedrich; Schneider, Gisbert.
Afiliación
  • Hähnke V; Johann Wolfgang-Goethe University, Frankfurt am Main 60323, Germany.
J Comput Chem ; 31(15): 2810-26, 2010 Nov 30.
Article en En | MEDLINE | ID: mdl-20839306
Previously, (Hähnke et al., J Comput Chem 2009, 30, 761) we presented the Pharmacophore Alignment Search Tool (PhAST), a ligand-based virtual screening technique representing molecules as strings coding pharmacophoric features and comparing them by global pairwise sequence alignment. To guarantee unambiguity during the reduction of two-dimensional molecular graphs to one-dimensional strings, PhAST employs a graph canonization step. Here, we present the results of the comparison of 11 different algorithms for graph canonization with respect to their impact on virtual screening. Retrospective screenings of a drug-like data set were evaluated using the BEDROC metric, which yielded averaged values between 0.4 and 0.14 for the best-performing and worst-performing canonization technique. We compared five scoring schemes for the alignments and found preferred combinations of canonization algorithms and scoring functions. Finally, we introduce a performance index that helps prioritize canonization approaches without the need for extensive retrospective evaluation.
Asunto(s)

Texto completo: 1 Colección: 01-internacional Banco de datos: MEDLINE Asunto principal: Bases de Datos Factuales / Alineación de Secuencia / Biología Computacional / Bibliotecas de Moléculas Pequeñas / Descubrimiento de Drogas Idioma: En Revista: J Comput Chem Asunto de la revista: QUIMICA Año: 2010 Tipo del documento: Article País de afiliación: Alemania

Texto completo: 1 Colección: 01-internacional Banco de datos: MEDLINE Asunto principal: Bases de Datos Factuales / Alineación de Secuencia / Biología Computacional / Bibliotecas de Moléculas Pequeñas / Descubrimiento de Drogas Idioma: En Revista: J Comput Chem Asunto de la revista: QUIMICA Año: 2010 Tipo del documento: Article País de afiliación: Alemania