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@durrantlab

Durrant Lab

The Durrant lab at the University of Pittsburgh develops and applies broadly applicable, innovative techniques for computer-aided drug discovery.

Popular repositories

  1. gypsum_dl 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, tauto…

    Python 29 10

  2. autogrow4 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…

    Python 22 9

  3. deepfrag 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 th…

    Python 11 4

  4. dimorphite_dl 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 sma…

    Python 10 6

  5. subpex 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 accel…

    Python 9 1

  6. pyrite 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…

    Python 8 1

Repositories

Showing 10 of 32 repositories
  • 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 9 MIT 1 0 1 Updated May 18, 2024
  • EnOpt Public

    Ensemble Optimizer (EnOpt) is a fast, accessible tool that streamlines ensemble-docking and consensus-score analysis.

    Python 0 MIT 0 0 0 Updated May 15, 2024
  • censible Public
    Jupyter Notebook 0 GPL-3.0 1 1 0 Updated May 11, 2024
  • molmoda Public

    MolModa provides a secure, accessible environment where users can perform molecular docking entirely in their web browsers.

    JavaScript 0 GPL-2.0 0 2 0 Updated May 10, 2024
  • wisp Public

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

    Python 2 AFL-3.0 0 1 0 Updated May 8, 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 29 Apache-2.0 10 2 1 Updated Apr 30, 2024
  • Makefile 0 0 0 0 Updated Apr 13, 2024
  • colab-support-files Public

    A place to put files for easy download into Google Colab.

    Jupyter Notebook 0 1 0 0 Updated Mar 28, 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 10 Apache-2.0 6 1 1 Updated Mar 15, 2024
  • Jupyter Notebook 0 GPL-3.0 1 0 0 Updated Jan 12, 2024