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1. pl4 pl4 Public

   A collection of notebooks for cloud docking, simulation, designing and evaluating new medicinal analogues.

   Jupyter Notebook

2. pl3_gmx_mmpbsa pl3_gmx_mmpbsa Public

   Open-Sourced. MMPBSA calculation and binding pocket residue-based energy decomposition after pl3 docking, with gmx_mmpbsa.

   Jupyter Notebook

3. Dock-MD-FEP Dock-MD-FEP Public

   Open Source, Automated free binding free energy calculation between protein and small molecule. An all-in-one workflow, free energy pertubation with OpenMM.

   Jupyter Notebook 51 11

4. Ambertools-OpenMM-MD Ambertools-OpenMM-MD Public

   Open Source, Mostly just clicking mouse to finish a simulation with Ambertools and OpenMM. It was designed to use locally but another notebook to finish the simulaiton on Colab was attached as well.

   Jupyter Notebook 34 6

5. labodock_binder labodock_binder Public

   Open-sourced docking for small molecule to protein target. It prioritizes enhanced user-friendliness and accessibility.

   Jupyter Notebook 5 3

6. Dock-MD-BPMD Dock-MD-BPMD Public

   Open-sourced. A cloud-based workflow to evaluate the confidence of a given docked pose with binding pose metadynamics

   Jupyter Notebook 3 1