MICLOT (Molecular InteraCtion anaLysis tOolkiT) is a collection of tools for analyzing protein-protein interactions in PDB files as well as MD simulations.
It was designed as a Python package to be integrated into user scripts, with the goal of providing a simple and flexible user experience with efficient tools. MICLOT comprises several key components:
- A database containing the physical and chemical properties of amino acids, as well as physical properties of elements (atoms) found in amino acids.
- Protocols for energy calculation, including one to calculate the Coulomb and Lennard-Jones energies of a pair of residues, and another to compute the binding energy of a protein complex.
- Identification of the non-bonding interactions (H-bonds, Pi-Pi stacking, ...) formed by a pair of residues.
- Functions to detect Cys-Cys bridges in a structure, featuring two protocols to detect disulfide bridges, as well as the ability to identify non-canonical bridges involving diselenium bonds (Se-Se) and selenosulfide bonds (Se-S).
- A set of utilities to work with structures.
- Tools to assist users in data analysis (under development).
mindmap
root)**MICLOT**(
id{{**Structural information**}}
Protein region
Secondary structure
id{{**Energy calculation**}}
Contacts-based method
Coulomb and Lennard-Jones
id{{**Cys-Cys bridge**}}
Disulfide
Diselenium
Selenosulfide
id{{**Non-bonded interactions**}}
id{{**Database**}}
Amino acids
Atoms
- For detailed instructions on installation, as well as information on the technical features and theoretical background of the software, please refer to the User guide.
- To begin exploring the capabilities of MICLOT, we recommend starting with the Tutorials, which provide a hands-on introduction to the software.
Currently, we do not have a formal protocol in place for bug report. So please simply send an email to [email protected]
The article is in preparation, please wait to cite our software.
Made with ❤️ by Tom Miclot