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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.

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  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 40 12

  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 29 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 18 5

  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 17 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 13 1

  6. binana binana Public

    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 inter…

    Jupyter Notebook 12 1

Repositories

Showing 10 of 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.

    durrantlab/autogrow4’s past year of commit activity
    Python 29 Apache-2.0 9 4 0 Updated Sep 12, 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.

    durrantlab/scoria’s past year of commit activity
    Python 2 Apache-2.0 0 0 0 Updated Aug 30, 2024
  • molmoda Public

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

    durrantlab/molmoda’s past year of commit activity
    JavaScript 9 GPL-2.0 2 3 0 Updated Aug 14, 2024
  • EnOpt Public

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

    durrantlab/EnOpt’s past year of commit activity
    HTML 4 MIT 0 0 0 Updated Aug 1, 2024
  • wisp Public

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

    durrantlab/wisp’s past year of commit activity
    Python 3 AFL-3.0 0 2 0 Updated Jun 29, 2024
  • colab-support-files Public

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

    durrantlab/colab-support-files’s past year of commit activity
    Jupyter Notebook 1 1 0 0 Updated May 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.

    durrantlab/subpex’s past year of commit activity
    Python 13 MIT 1 0 0 Updated May 22, 2024
  • censible Public
    durrantlab/censible’s past year of commit activity
    Jupyter Notebook 9 GPL-3.0 1 0 0 Updated May 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.

    durrantlab/gypsum_dl’s past year of commit activity
    Python 40 Apache-2.0 12 2 1 Updated Apr 30, 2024
  • molmoda-docs Public
    durrantlab/molmoda-docs’s past year of commit activity
    Makefile 0 0 0 0 Updated Apr 13, 2024
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