PD Dr. Oliver Koch

© Dziemba

Topics of research

The research interests of the working group Koch lie in the development and application of computational methods for the rational molecular design of new bioactive compounds. In an interdisciplinary way, the in-silico work is combined with biochemical evaluation for the identification and optimisation of promising molecules and the evaluation of newly developed methods. The range of applied computational methods includes well-known structure- and ligand-based methods such as docking, pharmacophore-searches and virtual screening, homology modelling, quantitative structure activity relationships and molecular dynamics simulation for a detailed characterization of protein structures. The new developed methods and approaches focus on the analysis of protein-ligand interactions and the underlying framework, and how to use the available amount of ‘big’ bioactivity data and protein structures for computational molecular design and optimisation.

ChemBIon project description

In-silico studies of ion channels using molecular dynamics simulation and computational molecular design with focus on KCa3.1 and HCN channels
In the last decades, computational molecular design has emerged as an essential research field for the analysis and the design of small molecule modulators of protein function. Due to the membrane embedded nature of ion channels X-ray structures are not easily accessible. Cryo-EM structures are also of limited use for the design of modulators due to their low resolution. Therefore, a detailed analysis and understanding of ion channels using molecular dynamics (MD) simulation is needed to provide reliable conformations for the application of computational molecular design methods like docking.
Objective: The goal of this project is to provide a detailed understanding of the binding mode of available KCa3.1 and HCN channel modulators based on MD simulations, structural modelling and experimental validation. The results will be used for structure-based design and for virtual screening approaches to advance the development and identification of modulators.

  • Curriculum vitae

    Short CV


    01/2019 – until today

    Independent Group Leader
    “Computational Medicinal Chemistry and Molecular Design” Institute of Pharmaceutical and Medicinal Chemistry, Westfälische Wilhelms-Universität Münster

    01/2019 – until today

    Associated Partner German Center for Infection Research(DZIF,www.dzif.de)

    10/2012 – 11/2018

    Independent Junior Group Leader „Medicinal Chemistry“, Faculty of Chemistry and Chemical Biology, TU Dortmund University

    08/2008 – 07/2012

    Scientist Computational Sciences / Molecular Discovery Sciences MSD Animal Health Innovation GmbH, Schwabenheim, Germany

    10/2007 – 07/2008

    Post-Doctoral Fellowship & Scientific Software Engineer

    The Cambridge Crystallographic Data Centre, Cambridge, UK



    University Education

    04/2003 – 09/2007

    Ph.D. student with Prof. Dr. G. Klebe
    Institute of pharmaceutical chemistry
    Philipps-Universität Marburg, Germany

    04/2004 – 09/2007

    Postgraduate Studies Computer Science
    with focus on machine learning
    Philipps-Universität Marburg, Germany


    Final pharmaceutical examination
    with following granted license to practice pharmacy

    07/2002 – 12/2002

    Pharmacist practical training (‘Pharmaziepraktikant’)
    Working Group Prof. Dr. G. Klebe
    Institute of Pharmaceutical Chemistry

    1997 - 2001

    Study of Pharmacy
    Philipps-Universität Marburg, Germany