LoCoMock

The LoCoMock score is useful in docking simulation for membrane protein.

It use membrane position and logP to validate docking poses.

DEMO

Features

Requirement (validated version)

• 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)

Installation

Install AutoDock, JupyterDock, and other required packages. Place LoCoMock_std.ipynb in the directory "Jupyter_Dock".

Usage

Launch LoCoMock_std.ipynb.

Place PDB files for protein (protein.pdb) and ligand (ligand.pdb) in the ./LoCoMock/{str_id} .

Note

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]

Author

• Rikuri Morita*, Yasuteru Shigeta, Ryuhei Harada*.
• Center for Computational Sciences, University of Tsukuba
• [email protected]

License

LoCoMock is a modified extension of Jupyter_Dock[https://github.com/AngelRuizMoreno/Jupyter_Dock].

LoCoMock is under MIT license.