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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.

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.

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.

LigGrep is a free, open-source program for identifying docked poses that participate in user-specified receptor/ligand interactions. As input, LigGrep accepts a protein receptor file (PDB, PDBQT), a directory containing many docked-compound files (PDB, PDBQT, SDF), and a list of user-specified filters (JSON). It evaluates each docked pose and outputs the names of the compounds with poses that pass all filters.

POVME2 (POcket Volume MEasurer 2.0) scans a molecular-dynamics simulation and extracts druggable protein pockets with unique conformations. It is useful because ligand-binding pockets adopt many conformations in response to atomic forces. Characterizing these pocket geometries helps identify those that are particularly amenable to ligand binding. Computer-aided drug-discovery campaigns that incorporate these conformations often identify novel pharmacologically active molecules.

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.

Scoria is a Python package for manipulating three dimensional molecular data. Unlike similar packages, Scoria is written in pure Python and so requires no dependencies or installation. One can incorporate the Scoria source code directly into their own programs. But Scoria is not designed to compete with other similar packages. Rather, it complements them. Our package leverages others (e.g., NumPy, SciPy, MDAnalysis), if present, to speed and extend its own functionality.

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 app. The app includes a convenient interface so users can easily setup their docking runs and analyze the results.