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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. 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 7 2

  2. 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 4 1

  3. 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 4

  4. 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 3 1

  5. 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 3 1

  6. 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 r…

    Python 3

Repositories

Showing 10 of 24 repositories
  • 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 1 Apache-2.0 0 0 0 Updated Sep 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 0 GPL-3.0 0 0 0 Updated Sep 9, 2023
  • wisp Public

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

    Python 0 0 0 0 Updated Jul 9, 2023
  • autogrow Public
    Python 0 0 0 0 Updated Jul 3, 2023
  • 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 4 MIT 0 0 0 Updated Jul 3, 2023
  • pcaviz Public
    JavaScript 1 GPL-2.0 1 0 0 Updated Jul 3, 2023
  • hbonanza Public
    Python 0 0 0 0 Updated Jul 3, 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 3 GPL-3.0 0 0 0 Updated Jul 3, 2023
  • 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 3 Apache-2.0 1 0 0 Updated Jul 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 0 GPL-3.0 0 0 0 Updated Jul 3, 2023
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