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1. Pymol_Script Pymol_Script Public

   A python script for PyMol to make protein-ligand interaction images.

   Python 3 1

2. labodock_binder labodock_binder Public

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

   Jupyter Notebook 3 2

3. openmm.py openmm.py Public

   Open-Sourced: Python script of openmm simulation. For GPU-accelerated molecular dynamics for protein-ligand complex.

   Jupyter Notebook 3 1

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 46 8

5. 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 30 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 1