3D-Sensitive Encoding of Pharmacophore Features.
J Chem Inf Model
; 63(8): 2360-2369, 2023 04 24.
Article
em En
| MEDLINE
| ID: mdl-37036083
ABSTRACT
In the presence of structural data, one sometimes need to compare 3D ligands. We design an overlay-free method to rank order 3D molecules in the pharmacophore feature space. The proposed encoding includes only two fittable parameters, is sparse, and is not too high dimensional. At the cost of an additional parameter, to delineate the binding site from a protein-ligand complex, the method can compare binding sites. The method was benchmarked on the LIT-PCBA data set for ligand-based virtual screening experiments and the sc-PDB and a Vertex data set when comparing binding sites. In similarity searches, the proposed method outperforms an open-source software doing optimal superposition of ligand-based pharmacophores and RDKit's 3D pharmacophore fingerprints. When comparing binding sites, the method is competitive with state of the art approaches. On a single CPU core, up to 374,000 ligand/s or 132,000 binding site/s can be rank ordered. The "AutoCorrelation of Pharmacophore Features" open-source software is released at https//github.com/tsudalab/ACP4.
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Software
/
Farmacóforo
Tipo de estudo:
Diagnostic_studies
Idioma:
En
Revista:
J Chem Inf Model
Assunto da revista:
INFORMATICA MEDICA
/
QUIMICA
Ano de publicação:
2023
Tipo de documento:
Article
País de afiliação:
Japão