A new web server, KBbox, provides a toolbox of computational methods for studying the kinetics of molecular binding
Recent research has shown that a better understanding of molecular binding kinetics is closely related to the efficacy of drugs and can affect drug properties such as selectivity and multi-target potency. Its importance has also become more recognized in systems biology modeling, where kinetic data are used to understand and model processes. The development of computational methods to study binding kinetics is thus an area of high current interest in the scientific community.
In order to provide an overview of the rapidly increasing number of computational methods for studying the kinetics of binding processes, the Molecular and Cellular Modeling (MCM) group at HITS has developed a web server that helps researchers decide which method might be suitable for their projects. Kbbox, which was developed with the support of the EU’s K4DD IMI and the Human Brain Project, allows users to choose the right method on the basis of the information they wish to obtain, the data they currently have available, and the computational resources to which they have access. KBbox is described in a recent publication in the American Chemical Society’s Journal of Chemical Information and Modeling (https://pubs.acs.org/doi/10.1021/acs.jcim.9b00485).
KBbox is freely available to all users without any login requirement at https://kbbox.h-its.org/ and provides up-to-date information on the toolbox of available methods, their associated software tools and an expanding list of curated examples of published applications. Supplementary tutorials explain how to apply some of the methods step by step.
KBbox has been designed to allow active updating, and the community is encouraged to submit novel methods, software, or new tutorials describing how they can be used. This can be done via the “Contact” section of KBbox, where templates are available for providing data, or via email.
KBbox: A Toolbox of Computational Methods for Studying the Kinetics of Molecular Binding
Neil J. Bruce, Gaurav K. Ganotra, Stefan Richter, and Rebecca C. Wade
Journal of Chemical Information and Modeling Article ASAP
HITS, the Heidelberg Institute for Theoretical Studies, was established in 2010 by physicist and SAP co-founder Klaus Tschira (1940-2015) and the Klaus Tschira Foundation as a private, non-profit research institute. HITS conducts basic research in the natural, mathematical, and computer sciences. Major research directions include complex simulations across scales, making sense of data, and enabling science via computational research. Application areas range from molecular biology to astrophysics. An essential characteristic of the Institute is interdisciplinarity, implemented in numerous cross-group and cross-disciplinary projects. The base funding of HITS is provided by the Klaus Tschira Foundation.