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 (3.10.9)
- matplotlib (3.6.3)
- numpy (1.23.5)
- py3dmol (2.0.1)
- vina (1.2.3)
- openbabel (3.1.1)
- rdkit (2022.09.4)
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. Efficient Screening of Protein-Ligand Complexes in Lipid Bilayers Using LoCoMock Score. (2023) J. Comput. Aided Mol. Des. DOI:[https://doi.org/10.1007/s10822-023-00502-8]
- Rikuri Morita*, Yasuteru Shigeta, Ryuhei Harada*.
- Center for Computational Sciences, University of Tsukuba
- morita@ccs.tsukuba.ac.jp
LoCoMock is a modified extension of Jupyter_Dock[https://github.com/AngelRuizMoreno/Jupyter_Dock].
LoCoMock is under MIT license.