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    32 repositories

    • fpdb

      Public
      fetch PDB database information
      Python
      •
      MIT License
      •1•0•0•0•Updated Aug 1, 2025Aug 1, 2025

    • db2_converter

      Public
      Python
      •0•0•0•0•Updated Jul 8, 2025Jul 8, 2025

    • wB97X-ML

      Public
      Robust machine learning interatomic potentials (MLIPs) that achieve accuracy comparable to the ωB97X-D3BJ/def2-TZVPP quantum mechanical method on non-covalent interactions.
      Python
      •
      MIT License
      •0•0•0•0•Updated Jun 18, 2025Jun 18, 2025

    • PDB-FRAGID

      Public
      3.15 million representative non-covalent dimers and energies from the PDB
      MIT License
      •0•0•0•0•Updated May 30, 2025May 30, 2025

    • SWDOCKP2_example

      Public
      A computation example of SWDOCKP2 x86 version.
      TeX
      •0•0•0•0•Updated May 16, 2025May 16, 2025

    • SUBDOCK

      Public
      DOCK submit-related scripts with restart mechanism, supporting SGE, SLURM, GNU parallel and charity engine platform.
      Shell
      •5•0•0•0•Updated Apr 29, 2025Apr 29, 2025

    • PDBBind-Opt

      Public
      Workflow to clean up and fix structural problems in protein-ligand binding datasets
      Jupyter Notebook
      •8•0•0•0•Updated Nov 5, 2024Nov 5, 2024

    • BindingNet

      Public
      Jupyter Notebook
      •
      MIT License
      •2•25•0•0•Updated Jul 3, 2024Jul 3, 2024

    • MetalDock

      Public
      Dock organometallic compounds to proteins/DNA/biomolecules
      Python
      •
      MIT License
      •7•0•0•0•Updated May 24, 2024May 24, 2024

    • TorsionNet

      Public
      A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM
      Jupyter Notebook
      •
      MIT License
      •16•0•0•0•Updated Mar 29, 2024Mar 29, 2024

    • pydock3

      Public
      Python package wrapping the DOCK Fortran program and providing several tools built on top of it.
      Fortran
      •
      Other
      •3•0•1•0•Updated Mar 6, 2024Mar 6, 2024

    • FAST

      Public
      Fusion models for Atomic and molecular STructures (FAST)
      Python
      •
      MIT License
      •30•0•0•0•Updated Oct 12, 2023Oct 12, 2023

    • Amber_beginning

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated May 17, 2023May 17, 2023

    • generalization_benchmark

      Public
      Jupyter Notebook
      •
      MIT License
      •0•9•1•0•Updated Nov 30, 2022Nov 30, 2022

    • benchmark_DOCK_Vina

      Public
      Jupyter Notebook
      •0•2•0•0•Updated Jul 7, 2022Jul 7, 2022

    • AutoDock-Vina

      Public
      AutoDock Vina
      C++
      •
      Apache License 2.0
      •254•0•0•0•Updated Jul 26, 2021Jul 26, 2021

    • rdkit

      Public
      The official sources for the RDKit library
      HTML
      •
      BSD 3-Clause "New" or "Revised" License
      •938•0•0•1•Updated Jul 1, 2021Jul 1, 2021

    • Wyz_graduate_design_code

      Public
      some scripts
      Python
      •0•0•0•0•Updated Jun 1, 2021Jun 1, 2021

    • openff-toolkit

      Public
      The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools. Documentation available at http://open-forcefield-toolkit.readthedocs.io
      Jupyter Notebook
      •
      MIT License
      •101•0•0•0•Updated Mar 26, 2021Mar 26, 2021

    • dgl-lifesci

      Public
      Python package for graph neural networks in chemistry and biology
      Python
      •
      Apache License 2.0
      •160•0•0•0•Updated Mar 14, 2021Mar 14, 2021

    • can-ai-do

      Public
      Predicting or pretending: artificial intelligence for protein-ligand interactions lack of sufficiently large and unbiased datasets
      project
      UnrealScript
      •
      MIT License
      •3•12•0•0•Updated Feb 21, 2021Feb 21, 2021

    • teachopencadd

      Public
      TeachOpenCADD: a teaching platform for computer-aided drug design (CADD) using open source packages and data
      Jupyter Notebook
      •
      Creative Commons Attribution 4.0 International
      •214•0•0•0•Updated Jan 13, 2021Jan 13, 2021

    • db2mol2

      Public
      Convert DB2 file back to Mol2. That could be useful in db2 development or other application.
      SQLPL
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Jan 8, 2021Jan 8, 2021

    • gnina

      Public
      A deep learning framework for molecular docking
      C++
      •
      Apache License 2.0
      •163•0•0•0•Updated Dec 9, 2020Dec 9, 2020

    • oddt

      Public
      Open Drug Discovery Toolkit
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •122•0•0•0•Updated Dec 2, 2020Dec 2, 2020

    • qvina

      Public
      Accurately speed up AutoDock Vina
      C++
      •
      Apache License 2.0
      •49•0•0•0•Updated Sep 12, 2020Sep 12, 2020

    • dpgen

      Public
      The deep potential generator
      Python
      •
      GNU Lesser General Public License v3.0
      •184•0•0•0•Updated Aug 14, 2020Aug 14, 2020

    • dpdata

      Public
      Manipulating DeePMD-kit, VASP, LAMMPS data formats.
      Python
      •
      GNU Lesser General Public License v3.0
      •151•0•0•0•Updated Aug 14, 2020Aug 14, 2020

    • deepmd-kit

      Public
      A deep learning package for many-body potential energy representation and molecular dynamics
      C++
      •
      GNU Lesser General Public License v3.0
      •569•0•0•0•Updated Aug 14, 2020Aug 14, 2020

    • flexible-docking

      Public
      GLSL
      •0•1•0•0•Updated Oct 10, 2019Oct 10, 2019