Dock-MD-BPMD

This is a three-step workflow based on the cloud to help you increase the confidence of a docked pose of a small molecule bound to a target protein. To achieve this, two aspects of the puzzle are needed,

• The algorithm or software if you like, for this end, this repository relies on all open-sourced packages,
• The hardware or platforms, for this, this workflow depends on the free Binder platform and the paid Google Colab GPU serice.

1. Docking with labodock_binder on Binder

(free service, only CPU required)

Note, in most cases people would use a PDB id that has been registered in the PDB bank, but if you have an in-house receptor, use this variation. https://colab.research.google.com/github/quantaosun/labodock_binder/blob/main/labodock_native_interaction/wedock_mac_local_receptor_native_interaction.ipynb

2. Amber inputs generation on Binder

(free service, only CPU required)

3. Binding pose metadynamics with OpenBPMD on Colab

(paid service, GPU required, V100 or above)

Credits/References//Platforms

1. https://github.com/quantaosun/labodock_binder
2. https://github.com/RyanZR/labodock
3. https://github.com/pablo-arantes/making-it-rain
4. Arantes P.R., Depólo Polêto M., Pedebos C., Ligabue-Braun R. Making it rain: cloud-based molecular simulations for everyone. Journal of Chemical Information and Modeling 2021. DOI: 10.1021/acs.jcim.1c00998.
5. A. J. Clark, P. Tiwary, K. Borrelli, S. Feng, E. Miller, R. Abel, R. A. Friesner, B. J. Berne, J. Chem. Theory Comput. 2016, 12, 6, 2990–2998, DOI:https://doi.org/10.1021/acs.jctc.6b00201
6. D. Lukauskis, M. L. Samways, S. Aureli, B. P. Cossins, R. D. Taylor, F. L. Gervasio, J. Chem. Inf. Model. 2022, 62, 23, 6209–6216, DOI:https://doi.org/10.1021/acs.jctc.6b00201
7. https://mybinder.org/
8. https://colab.research.google.com/