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ASEDock-Docking Based on Alpha Spheres and Excluded Volumes

Goto, Junichi ; Kataoka, Ryoichi ; Muta, Hajime ; Hirayama, Noriaki

Journal of chemical information and modeling, 2008-03, Vol.48 (3), p.583-590 [Periódico revisado por pares]

United States: American Chemical Society

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  • Título:
    ASEDock-Docking Based on Alpha Spheres and Excluded Volumes
  • Autor: Goto, Junichi ; Kataoka, Ryoichi ; Muta, Hajime ; Hirayama, Noriaki
  • Assuntos: Biochemistry ; Bioinformatics ; Experiments ; Ligands ; Models, Molecular ; Protein Binding ; Proteins ; Proteins - chemistry
  • É parte de: Journal of chemical information and modeling, 2008-03, Vol.48 (3), p.583-590
  • Notas: istex:25B208A4D959D26F737A75E53794C7096C3558AD
    ark:/67375/TPS-P70N52JQ-H
    ObjectType-Article-1
    SourceType-Scholarly Journals-1
    ObjectType-Feature-2
  • Descrição: ASEDock is a novel docking program based on a shape similarity assessment between a concave portion (i.e., concavity) on a protein and the ligand. We have introduced two novel concepts into ASEDock. One is an ASE model, which is defined by the combination of alpha spheres generated at a concavity in a protein and the excluded volumes around the concavity. The other is an ASE score, which evaluates the shape similarity between the ligand and the ASE model. The ASE score selects and refines the initial pose by maximizing the overlap between the alpha spheres and the ligand, and minimizing the overlap between the excluded volume and the ligand. Because the ASE score makes good use of the Gaussian-type function for evaluating and optimizing the overlap between the ligand and the site model, it can pose a ligand onto the docking site relatively faster and more effectively than using potential energy functions. The posing stage through the use of the ASE score is followed by full atomistic energy minimization. Because the posing algorithm of ASEDock is free from any bias except for shape, it is a very robust docking method. A validation study using 59 high-quality X-ray structures of the complexes between drug-like molecules and the target proteins has demonstrated that ASEDock can faithfully reproduce experimentally determined docking modes of various druglike molecules in their target proteins. Almost 80% of the structures were reconstructed within the estimated experimental error. The success rate of ∼98% was attained based on the docking criterion of the root-mean-square deviation (RMSD) of non-hydrogen atoms (≤2.0 Å). The markedly high success of ASEDock in redocking experiments clearly indicates that the most important factor governing the docking process is shape complementarity.
  • Editor: United States: American Chemical Society
  • Idioma: Inglês
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  • Realização: ABCD-USP USP   Logos de Redes Sociais: Freepik

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