Pinned

1. labodock_binder labodock_binder Public

   Open-sourced, this workflow stands out as one of the premier methods for generating protein-ligand interaction images. With direct accessibility through your browser, it prioritizes enhanced user-…

   Jupyter Notebook 2 1

2. 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. 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 27 3

4. 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 1

5. 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 40 7

6. FEP-Minus FEP-Minus Public

   Academic license pre-required. While FEP Plus charge you 100,000 USD per year. Here comes the FEP-Minus, it is a Schrodinger FEP Plus identical calculation but for FREE (Only for Academic community…

   Jupyter Notebook 17 1