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    32 repositories

    • 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 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.
      Python
      •
      Apache License 2.0
      •9•29•4•0•Updated Oct 19, 2024Oct 19, 2024

    • 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
      •2•9•3•0•Updated Oct 13, 2024Oct 13, 2024

    • scoria

      Public
      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.
      Python
      •
      Apache License 2.0
      •0•2•0•0•Updated Aug 30, 2024Aug 30, 2024

    • EnOpt

      Public
      Ensemble Optimizer (EnOpt) is a fast, accessible tool that streamlines ensemble-docking and consensus-score analysis.
      HTML
      •
      MIT License
      •0•4•0•0•Updated Aug 1, 2024Aug 1, 2024

    • wisp

      Public
      WISP is a trajectory analysis tool that calculates and visualizes allosteric pathways.
      Python
      •
      Academic Free License v3.0
      •0•3•2•0•Updated Jun 29, 2024Jun 29, 2024

    • colab-support-files

      Public
      A place to put files for easy download into Google Colab.
      Jupyter Notebook
      •1•1•0•0•Updated May 24, 2024May 24, 2024

    • 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 molecular dynamics simulations to accelerate binding-pocket sampling.
      Python
      •
      MIT License
      •1•14•0•0•Updated May 22, 2024May 22, 2024

    • censible

      Public
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •1•9•0•0•Updated May 11, 2024May 11, 2024

    • gypsum_dl

      Public
      Gypsum-DL is a free, open-source program that converts 1D and 2D small-molecule representations (SMILES strings or flat SDF files) into 3D models. It outputs models with alternate ionization, tautomeric, chiral, cis/trans isomeric, and ring-conformational states.
      Python
      •
      Apache License 2.0
      •12•43•2•1•Updated Apr 30, 2024Apr 30, 2024

    • molmoda-docs

      Public
      Makefile
      •
      Other
      •0•0•0•0•Updated Apr 13, 2024Apr 13, 2024

    • dimorphite_dl

      Public
      Dimorphite-DL adds hydrogen atoms to molecular representations, as appropriate for a user-specified pH range. It is a fast, accurate, accessible, and modular open-source program for enumerating small-molecule ionization states.
      Python
      •
      Apache License 2.0
      •6•18•2•1•Updated Mar 15, 2024Mar 15, 2024

    • censible_base

      Public
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Jan 12, 2024Jan 12, 2024

    • 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 extension is also highly complementary to the receptor. The DeepFrag web application is also a useful tool for teaching students about medicinal chemistry and lead optimization.
      Python
      •
      Apache License 2.0
      •5•20•2•0•Updated Dec 22, 2023Dec 22, 2023

    • 3Dmol.js

      Public
      WebGL accelerated JavaScript molecular graphics library
      Jupyter Notebook
      •
      Other
      •194•0•0•0•Updated Dec 22, 2023Dec 22, 2023

    • molgriddebug

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Dec 12, 2023Dec 12, 2023

    • blendmol

      Public
      BlendMol is a Blender plugin that can easily import VMD 'Visualization State' files. BlendMol empowers scientific researchers and artists by marrying molecular visualization and industry-standard rendering techniques. The plugin works seamlessly with a popular analysis program (VMD).
      Python
      •
      GNU General Public License v3.0
      •1•7•0•0•Updated Oct 17, 2023Oct 17, 2023

    • nnscore2

      Public
      Python
      •0•2•0•0•Updated Oct 8, 2023Oct 8, 2023

    • deepfrag-app

      Public
      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. The DeepFrag web application is also a useful tool for teaching students about medicinal chemistry and lead optimization.
      TypeScript
      •
      Apache License 2.0
      •0•6•1•0•Updated Sep 16, 2023Sep 16, 2023

    • autoclickchem

      Public
      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•2•0•0•Updated Sep 9, 2023Sep 9, 2023

    • autogrow

      Public
      Python
      •0•1•0•0•Updated Jul 3, 2023Jul 3, 2023

    • pcaviz

      Public
      JavaScript
      •
      GNU General Public License v2.0
      •2•2•0•0•Updated Jul 3, 2023Jul 3, 2023

    • hbonanza

      Public
      Python
      •
      Other
      •0•0•0•0•Updated Jul 3, 2023Jul 3, 2023

    • POVME

      Public
      POVME2 (POcket Volume MEasurer 2) 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.
      Python
      •
      GNU General Public License v3.0
      •0•5•0•0•Updated Jul 3, 2023Jul 3, 2023

    • prot2prot

      Public
      Prot2Prot is a deep-learning model trained to imitate a Blender-rendered image given a much simpler representation ('sketch') of a protein surface. Prot2Prot outputs an image that is often indistinguishable from a Blender/BlendMol-based visualization in a fraction of the time, allowing image 'rendering' even in a web browser.
      TypeScript
      •
      Apache License 2.0
      •0•1•0•0•Updated Jul 3, 2023Jul 3, 2023

    • pyrite

      Public
      Pyrite is a Blender plugin that imports the atomic motions captured by molecular dynamics simulations. Using Pyrite, these motions can be rendered using Blender's state-of-the-art computer-graphics algorithms. All 3D protein representations (e.g., surface, ribbon, VDW spheres) are supported.
      Python
      •
      GNU General Public License v3.0
      •1•8•0•0•Updated Jul 3, 2023Jul 3, 2023

    • 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 protein receptor file (PDB, PDBQT), a directory containing many docked-compound files (PDB, PDBQT, SDF), and a list of user-specified filters (JSON).
      Python
      •
      Apache License 2.0
      •0•6•0•0•Updated Jul 3, 2023Jul 3, 2023

    • nnscore1

      Public
      Python
      •0•0•0•0•Updated Jul 3, 2023Jul 3, 2023

    • lipidwrapper

      Public
      Python
      •
      Other
      •0•0•0•0•Updated Jul 3, 2023Jul 3, 2023

    • 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 entirely in a web browser. The pocket-finding calculations occur on the user’s computer rather than a remote server.
      JavaScript
      •
      Apache License 2.0
      •0•0•0•0•Updated Jul 3, 2023Jul 3, 2023

    • webina

      Public
      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.
      TypeScript
      •
      Apache License 2.0
      •0•3•0•0•Updated Jul 3, 2023Jul 3, 2023