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 3 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 28 3

4. 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 39 7

5. 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

6. Maestro_to_CharmmGui Maestro_to_CharmmGui Public

   This is a simple repo to guide how to process the protein-ligand structures from Maestro (Schrodinger) to be recognised by the Charmm GUI platform (https://www.charmm-gui.org/).