WISP is a trajectory analysis tool that calculates and visualizes allosteric pathways.

A JavaScript/WebAssembly library that runs Vina in a browser. The calculations take place on the user's own computer. We have incorporated the Webina library into a new web app that helps users setup their docking runs and analyze the results.

Scoria is a Python package for manipulating 3D molecular data.

A Blender plugin for importing a molecular dynamics trajectory, to take advantage of Blender's advanced rendering features.

Browser-based, virtual-reality visualization of molecular structures.

Prot2Prot is a deep-learning model trained to imitate a Blender/BlendMol-rendered image given a much simpler representation (“sketch”) of a protein surface.

POVME2 (POcket Volume MEasurer 2) scans a molecular-dynamics simulation and extracts druggable protein pockets with unique conformations. Virtual screens that leverage these conformations often identify novel active molecules.

PCAViz is an open-source Python/JavaScript toolkit for sharing and visualizing molecular dynamics trajectories via a web browser.

NNScore is a scoring function for characterizing the potency of receptor-ligand complexes. It is based on neural networks, computational models that simulate the microscopic organization of the brain.

NNScore is a scoring function for characterizing the potency of receptor-ligand complexes. It is based on neural networks, computational models that simulate the microscopic organization of the brain.

LipidWrapper is a program for creating large-scale, curved membrane models of arbitrary size and geometry.

LigGrep is a program for identifying docked poses that participate in user-specified receptor/ligand interactions. It evaluates each docked pose and outputs the names of the compounds with poses that pass all filters.

A program for converting 2D SMILES strings to 3D models.

FpocketWeb is a browser app for identifying pockets on protein surfaces where small-molecule ligands (e.g., drugs) might bind. It runs the fpocket executable entirely in a web browser. The pocket-finding calculations occur on the user’s computer rather than a remote server.

Dimorphite-DL is a fast, accurate, accessible, and modular open-source program for enumerating small-molecule ionization states.

An easy to use, browser-based GUI for running DeepFrag. The goal is to suggest useful chemical changes to a small-molecule ligand that might improve its binding to a protein receptor (i.e., to aid lead optimization).

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.

Easily import VMD scenes into Blender.

BINANA analyzes docked ligand poses to identify molecular interactions that contribute to binding. Accurately characterizing these interactions allows medicinal chemists to assess whether a predicted ligand merits further study.