What MLCE are?

MLCE stands for Matrix of Lowest Coupling Energies and they can be used to represent the region of the protein lowest dynamically coupled. This means that they are also the most prone to be involved in interaction with external partners.

Mathematically speaking this process is an energy decomposition method, which starts with the calculation of the unbound part of the potential E (van der Waals, electrostatic interactions, solvent effects) through an MM/GBSA calculation:

Since the first eigenvector contains most of the relevant energy information about the interactions in the system, we can approximate the matrix energy to the first eigenvector:

Finally, we can filter the approximated interaction matrix Mio for residues that are in geometric proximity in the structure (closer than 6Å):

How to use the script

Please see the attached documentation files in Drive repository.

References

1. Scarbelli, G.; Morra, G.; Colombo, G., Predicting Interaction Sites from the Energetics of Isolated Proteins: A New Approach to Epitope Mapping, Biophys. J., 2010, 98, 1966, https://doi.org/10.1016%2Fj.bpj.2010.01.014

2. Genoni, A.; Morra, G.; Colombo, G., Identification of Domains in Protein Structures from the Analysis of Intramolecular Interactions, J. Phys. Chem. B, 2012, 116, 10, 3331–3343, https://doi.org/10.1021/jp210568a