DeepFrag

DeepFrag

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.



BINANA

BINANA

BINANA

BINANA (BINding ANAlyzer) analyzes the geometries of predicted ligand poses to identify molecular interactions that contribute to binding. It is useful because accurately characterizing these interactions allows medicinal chemists to assess whether a predicted ligand merits further study. We have also created a BINANA web-browser application so students and chemical-biology researchers can quickly visualize receptor/ligand complexes and their unique binding interactions.



Webina

Webina

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.



ProteinVR

ProteinVR

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.



PCAViz

PCAViz

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.