Classification of chemical compounds by protein-compound docking for use in designing a focused library.
J Med Chem
; 49(2): 523-33, 2006 Jan 26.
Article
em En
| MEDLINE
| ID: mdl-16420039
ABSTRACT
We developed a new method for the classification of chemical compounds and protein pockets and applied it to a random screening experiment for macrophage migration inhibitory factor (MIF). The principal component analysis (PCA) method was applied to the protein-compound interaction matrix, which was given by thorough docking calculations between a set of many protein pockets and chemical compounds. Each compound and protein pocket was depicted as a point in the PCA spaces of compounds and proteins, respectively. This method was applied to distinguish active compounds from negative compounds of MIF. A random screening experiment for MIF was performed, and our method revealed that the active compounds were localized in the PCA space of compounds, while the negative compounds showed a wide distribution. Furthermore, protein pockets, which bind similar compounds, were classified and were found to form a cluster in the PCA space.
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Base de dados:
MEDLINE
Assunto principal:
Compostos Orgânicos
/
Proteínas
/
Técnicas de Química Combinatória
/
Relação Quantitativa Estrutura-Atividade
Tipo de estudo:
Prognostic_studies
Idioma:
En
Revista:
J Med Chem
Assunto da revista:
QUIMICA
Ano de publicação:
2006
Tipo de documento:
Article
País de afiliação:
Japão