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    38 repositories

    • molmoda

      Public
      MolModa provides a secure, accessible environment where users can perform molecular docking entirely in their web browsers.
      JavaScript
      •
      GNU General Public License v2.0
      •6•20•5•0•Updated Apr 25, 2026Apr 25, 2026

    • POVME

      Public
      Detect and characterize binding pockets from molecular simulations.
      Python
      •
      GNU General Public License v3.0
      •3•16•0•0•Updated Mar 17, 2026Mar 17, 2026

    • metalflare

      Public
      metalflare: Investigating metal-sensing green fluorescent proteins
      Python
      •
      MIT License
      •0•1•0•0•Updated Feb 16, 2026Feb 16, 2026

    • deepfrag2

      Public
      Jupyter Notebook
      •
      MIT License
      •0•6•0•0•Updated Dec 16, 2025Dec 16, 2025

    • dimorphite_dl

      Public
      Adds or removes hydrogen atoms to achieve the appropriate molecular protonation state for a user-specified pH range
      Python
      •
      Apache License 2.0
      •14•63•3•0•Updated Dec 13, 2025Dec 13, 2025

    • gypsum_dl

      Public
      Open-source tool to generate 3D-ready small molecules for virtual screening
      Python
      •
      Apache License 2.0
      •19•81•5•1•Updated Nov 18, 2025Nov 18, 2025

    • autogrow4

      Public
      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 i…
      Python
      •
      Apache License 2.0
      •18•56•9•1•Updated Oct 7, 2025Oct 7, 2025

    • censible

      Public
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •1•9•0•0•Updated Jul 3, 2025Jul 3, 2025

    • wisp

      Public
      WISP is a trajectory analysis tool that calculates and visualizes allosteric pathways.
      Python
      •
      Academic Free License v3.0
      •2•8•2•0•Updated Jul 3, 2025Jul 3, 2025

    • 3Dmol.js

      Public
      WebGL accelerated JavaScript molecular graphics library
      Jupyter Notebook
      •
      Other
      •217•0•0•0•Updated Jul 2, 2025Jul 2, 2025

    • webina

      Public archive
      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 rat…
      TypeScript
      •
      Apache License 2.0
      •3•7•0•0•Updated Jun 30, 2025Jun 30, 2025

    • subpex

      Public
      SubPEx (Sub-Pocket Explorer) is a tool to enhance ensemble (multiple-receptor/relaxed-complex) virtual screening. It uses weighted ensemble path sampling and mo…
      Python
      •
      MIT License
      •1•18•0•0•Updated Jun 30, 2025Jun 30, 2025

    • scoria

      Public archive
      Scoria is a Python package for manipulating three dimensional molecular data. Unlike similar packages, Scoria is written in pure Python and so requires no depen…
      Python
      •
      Apache License 2.0
      •0•3•0•0•Updated Jun 30, 2025Jun 30, 2025

    • pyrite

      Public archive
      Pyrite is a Blender plugin that imports the atomic motions captured by molecular dynamics simulations. Using Pyrite, these motions can be rendered using Blender…
      Python
      •
      GNU General Public License v3.0
      •1•12•0•0•Updated Jun 30, 2025Jun 30, 2025

    • pymolecule

      Public archive
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jun 30, 2025Jun 30, 2025

    • protein-vr

      Public
      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…
      TypeScript
      •
      Other
      •1•5•0•0•Updated Jun 30, 2025Jun 30, 2025

    • prot2prot

      Public archive
      Prot2Prot is a deep-learning model trained to imitate a Blender-rendered image given a much simpler representation ('sketch') of a protein surface. Prot2Prot ou…
      TypeScript
      •
      Apache License 2.0
      •0•1•0•0•Updated Jun 30, 2025Jun 30, 2025

    • pcaviz

      Public archive
      JavaScript
      •
      GNU General Public License v2.0
      •2•2•0•0•Updated Jun 30, 2025Jun 30, 2025

    • nnscore2

      Public archive
      Python
      •2•3•0•0•Updated Jun 30, 2025Jun 30, 2025

    • nnscore1

      Public archive
      Python
      •0•0•0•0•Updated Jun 30, 2025Jun 30, 2025

    • molmoda-docs

      Public
      Makefile
      •
      Other
      •1•0•0•0•Updated Jun 30, 2025Jun 30, 2025

    • lipidwrapper

      Public archive
      Python
      •
      Other
      •2•1•0•0•Updated Jun 30, 2025Jun 30, 2025

    • liggrep

      Public
      LigGrep is a free, open-source program for identifying docked poses that participate in user-specified receptor/ligand interactions. As input, LigGrep accepts a…
      Python
      •
      Apache License 2.0
      •0•7•0•0•Updated Jun 30, 2025Jun 30, 2025

    • fpocketweb

      Public
      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 en…
      JavaScript
      •
      Apache License 2.0
      •2•4•0•0•Updated Jun 30, 2025Jun 30, 2025

    • EnOpt

      Public
      Ensemble Optimizer (EnOpt) is a fast, accessible tool that streamlines ensemble-docking and consensus-score analysis.
      HTML
      •
      MIT License
      •0•5•0•0•Updated Jun 30, 2025Jun 30, 2025

    • deepfrag

      Public
      DeepFrag is a deep convolutional neural network that guides ligand optimization by extending a ligand with a molecular fragment, such that the resulting extensi…
      Python
      •
      Apache License 2.0
      •6•30•2•0•Updated Jun 30, 2025Jun 30, 2025

    • blendmol

      Public archive
      BlendMol is a Blender plugin that can easily import VMD 'Visualization State' files. BlendMol empowers scientific researchers and artists by marrying molecular …
      Python
      •
      GNU General Public License v3.0
      •2•8•0•0•Updated Jun 30, 2025Jun 30, 2025

    • binana

      Public
      BINANA (BINding ANAlyzer) analyzes the geometries of predicted ligand poses to identify molecular interactions that contribute to binding. It is useful because …
      Jupyter Notebook
      •
      Apache License 2.0
      •2•24•2•0•Updated Jun 30, 2025Jun 30, 2025

    • autogrow

      Public archive
      Python
      •0•1•0•0•Updated Jun 30, 2025Jun 30, 2025

    • autoclickchem

      Public archive
      AutoClickChem simulates click-chemistry reactions in silico to create large compound libraries for virtual drug screening and streamlined real-world synthesis.
      Python
      •
      GNU General Public License v3.0
      •1•4•0•0•Updated Jun 30, 2025Jun 30, 2025
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