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1. 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 55 11

2. Zinc-Million Zinc-Million Public

   Open-Sourced. Millions of small molecules will be downloaded from the ZINC database in 3D SDF file format, with one click, to get ready for a large scale virtual screening for certain protein target.

   Jupyter Notebook 12 6

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 35 7

4. 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

5. Schrodinger_Docking_and_MD Schrodinger_Docking_and_MD Public

   Need Schroddinger license, Starting from a SMILES string and a PDB ID, here is an automatic knime workflow for docking then follwed by molecular dynamic. Integrates induced fit docking with MD to g…

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6. 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