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Quantum chemical associations ligand-residue: their role to predict flavonoid binding sites in proteins.
Rolo-Naranjo, Alberto; Codorniu-Hernández, Edelsys; Ferro, Noel.
Afiliação
  • Rolo-Naranjo A; Department of Molecular Design and Synthesis, Higher Institute of Technologies and Applied Sciences, Habana, Cuba.
J Chem Inf Model ; 50(5): 924-33, 2010 May 24.
Article em En | MEDLINE | ID: mdl-20373791
A novel approach is applied for the prediction of potential binding sites in ligand-protein interactions. This methodology introduces an integral strategy based on the calculation of protein geometrical parameters and the use of a quantum mechanical descriptor, Binding Local Site (B(LS)). A screening of the most likely cavities in the protein crystal structure is carried out where the analysis of geometric cavities is performed, and the virtual centers for binding (VCB) are located. The VCB surrounding amino acid residues (AA) are evaluated through the calculation of the B(LS) by using the theoretical affinity order between the ligand and each AA. It includes a quantum scoring function based on the ligand-AA association energies and entropies. A contribution to the understanding of flavonoid-protein interactions is provided as well. The new bioinformatic strategy makes good predictions for flavonoid ligands. The calculated binding sites are quite in agreement with the crystal binding sites of 10 flavonoid binding proteins. This is a contribution of quantum mechanics in some phases of in silico drug design.
Assuntos

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Flavonoides / Proteínas Tipo de estudo: Prognostic_studies / Risk_factors_studies Limite: Humans Idioma: En Revista: J Chem Inf Model Assunto da revista: INFORMATICA MEDICA / QUIMICA Ano de publicação: 2010 Tipo de documento: Article País de afiliação: Cuba País de publicação: Estados Unidos

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Flavonoides / Proteínas Tipo de estudo: Prognostic_studies / Risk_factors_studies Limite: Humans Idioma: En Revista: J Chem Inf Model Assunto da revista: INFORMATICA MEDICA / QUIMICA Ano de publicação: 2010 Tipo de documento: Article País de afiliação: Cuba País de publicação: Estados Unidos