We develop open-source tools for computer-aided drug discovery (CADD), focusing on molecular docking, dynamics, cheminformatics, and machine learning. Our research helps identify small-molecule ligands, study protein function, and accelerate therapeutic discovery.
Our tools are free to use and built for reproducibility, education, and extensibility. We welcome contributions and scientific collaborations.
Adds or removes hydrogen atoms to achieve the appropriate molecular protonation state for a user-specified pH range
MolModa provides a secure, accessible environment where users can perform molecular docking entirely in their web browsers.
AutoGrow4 is an open-source program for semi-automated computer-aided drug discovery. It uses a genetic algorithm to evolve predicted ligands on demand and so is not limited to a virtual library of pre-enumerated compounds. AutoGrow4 is a useful tool for generating entirely novel drug-like molecules and for optimizing preexisting ligands.
Adds or removes hydrogen atoms to achieve the appropriate molecular protonation state for a user-specified pH range
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.
SubPEx (Sub-Pocket Explorer) is a tool to enhance ensemble (multiple-receptor/relaxed-complex) virtual screening. It uses weighted ensemble path sampling and molecular dynamics simulations to accelerate binding-pocket sampling.
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