Explore projects

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.

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

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.

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

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).

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

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.

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.

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.

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.

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

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

AutoGrow4 is an open-source program for generating novel drug-like molecules and optimizing preexisting ligands. It uses a genetic algorithm to evolve predicted ligands.

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.

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

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

Easily import VMD scenes into Blender.

IMPORTANT NOTE: The latest version of AutoGrow (v4) can be found at http://git.durrantlab.com/jdurrant/autogrow4