Educational Tools

Many of our research tools have been implemented as easy-to-use browser apps that are well suited for even large classroom settings. Please let us know if you use any of our tools in your courses!

  • DeepFrag

    DeepFrag is a deep convolutional neural network that guides ligand optimization by extending a ligand with a molecular fragment, such that the resulting extension is also highly complementary to the receptor. The DeepFrag web application is also a useful tool for teaching students about medicinal chemistry and lead optimization.
  • PCAViz

    PCAViz is an open-source Python/JavaScript toolkit for sharing and visualizing MD trajectories via a web browser. It is also a helpful tool for class websites and presentations. To encourage use, an easy-to-install PCAViz-powered WordPress plugin enables ‘plug-and-play’ trajectory visualization.
  • ProteinVR

    ProteinVR is a web-based application that allows users to view protein/ligand structures in virtual reality (VR) from their mobile, desktop, or VR-headset-based web browsers. Molecular structures are displayed within 3D environments that give useful biological context and allow users to situate themselves in 3D space. We expect the ProteinVR web application to be useful in both research and classroom settings.
  • Webina

    Webina is a JavaScript/WebAssembly library that runs AutoDock Vina entirely in a web browser. The docking calculations take place on the user’s own computer rather than a remote server. To encourage use, we have incorporated the Webina library into our own Webina web application. The app includes a convenient interface so users can easily setup their docking runs and analyze the results. Aside from its research applications, Webina is an excellent tool for teaching students about computer-aided drug discovery, protein/ligand interactions, and computational structural biology.