The LoCoMock score is useful in docking simulation for membrane protein.
It use membrane position and logP to validate docking poses.
- Jupyter_Dock (v0.2.5)
- Python 3.x (3.7.10)
- matplotlib 3.4.3
- numpy 1.19.1
- py3dmol 0.9.2
- vina 1.2.2
- openbabel 3.1.1
- rdkit 2021.03.5
Install AutoDock, JupyterDock, and other required packages. Place LoCoMock_std.ipynb in the directory "Jupyter_Dock".
Launch LoCoMock_std.ipynb.
Place PDB files for protein (protein.pdb) and ligand (ligand.pdb) in the ./LoCoMock/{str_id} .
Please cite this paper.
Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada. LoCoMock: LogP-corrected Membrane Docking for Protein–Ligand Complexes. Submitted (2022)DOI:[https://doi.org/]
- Rikuri Morita*, Yasuteru Shigeta, Ryuhei Harada*.
- Center for Computational Sciences, University of Tsukuba
- [email protected]
LoCoMock is a modified extension of Jupyter_Dock[https://github.com/AngelRuizMoreno/Jupyter_Dock].
LoCoMock is under MIT license.