Optimal Overlay of Ligands with Flexible Bonds Using Differential Evolution

Thomas Greve Kristensen, Christian Storm Pedersen

    Publikation: Bidrag til bog/antologi/rapport/proceedingKonferencebidrag i proceedingsForskningpeer review

    Abstract

    When designing novel drugs, the need arise to screen large databases of drug candidates (small synthesizable chemical structures) for structures that resemble active ligands, i.e. small chemical structures that are known to react with the target protein. If several active ligands are known one might improve the quality of the search by taking all of these into account. This can be done by generating a meta-structure which summarizes the active ligands and use this meta-structure for querying the database. In this paper we propose a method for making such a meta-structure by making a multiple spatial alignment of a set of active ligands taking the flexibility of chemical bonds into account. We present two implementations of our method. One using Differential Evolution (DE) for numerical optimization, and one using the Nelder-Mead method for numerical optimization. We investigate the quality of the two implementations on a data set from a previous study in the field and conclude that the DE based implementation outperforms the NM based implementation.
    OriginalsprogEngelsk
    Titel Proceedings of the 2009 International Joint conferences on Bioinformatics, System biology and Intelligent Computing (IJCBS2009)
    RedaktørerJoe Zhang, G.-Z. Li, J.Y. Yang
    Antal sider4
    ForlagIEEE Computer Society Press
    Publikationsdato2009
    Sider331-334
    ISBN (Trykt)978-0-7695-3739-9
    DOI
    StatusUdgivet - 2009
    BegivenhedInternational Joint Conferences on Bioinformatics, Systems Biology and Intelligent Computing (IJCBS) - Shanghai, Kina
    Varighed: 3 aug. 20095 aug. 2009

    Konference

    KonferenceInternational Joint Conferences on Bioinformatics, Systems Biology and Intelligent Computing (IJCBS)
    Land/OmrådeKina
    ByShanghai
    Periode03/08/200905/08/2009

    Fingeraftryk

    Dyk ned i forskningsemnerne om 'Optimal Overlay of Ligands with Flexible Bonds Using Differential Evolution'. Sammen danner de et unikt fingeraftryk.

    Citationsformater