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  • Molecular dynamics to enhance structure-based virtual screening on cathepsin B
    Ogrizek, Mitja ...
    Molecular dynamics (MD) and molecular docking are commonly used to study molecular interactions in drug discovery. Most docking approaches consider proteins as rigid, which can decrease the accuracy ... of predicted docked poses. Therefore MD simulations can be used prior to docking to add flexibility to proteins. We evaluated the contribution of using MD together with docking in adocking study on human cathepsin B, a well-studied protein involved in numerous pathological processes. Using CHARMM biomolecular simulation program and AutoDock Vina molecular docking program, we found, that short MD simulations significantly improved molecular docking. Our results, expressed with the area under the receiver operating characteristic curves, show an increase in discriminatory power i.e. the ability to discriminate active from inactive compounds of molecular docking, when docking is performed to selectedsnapshots from MD simulations.
    Source: Journal of computer-aided molecular design. - ISSN 0920-654X (Vol. 29, iss. 8, 2015, str. 707-712)
    Type of material - article, component part
    Publish date - 2015
    Language - english
    COBISS.SI-ID - 3858033

    Link(s):

    http://link.springer.com/article/10.1007%2Fs10822-015-9847-2
    DOI

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