Analysis and visualize tool kit for FMO #FMO

I and my daughter got the flu last week and now we are staying in my home…
Now I read some articles and found interesting work for FMO.
URL is below.
https://pubs.acs.org/doi/10.1021/acs.jcim.8b00649
FMO means ‘Fragment Molecular Orbital’ that is powerful method for protein-ligand interaction energy calculation. Evotec which is a drug discovery alliance and development partnership company published many attractive articles about utilization of FMO for Drug design.
Some of examples are …
https://pubs.acs.org/doi/abs/10.1021/acs.jmedchem.6b00045
https://pubs.acs.org/doi/abs/10.1021/acs.jcim.5b00644
https://link.springer.com/protocol/10.1007%2F978-1-4939-7465-8_8
FMO is useful but lack of efficient analytical tool, it is difficult to understand the results for none specialist I think.

The authors developed new analysis and visualization tool kit for FMO RbAnalysisFMO and Pymol plugin written by Ruby and Python. Both tool kit s are freely available.
http://dfns.u-shizuoka-ken.ac.jp/labs/proeng/custom20.html/

This tool kit can analyze two modes, ‘All-pairs’ and ‘Selected-pairs’. All-pairs mode can analyze all pair IEIE or PIE and ‘Selected-piars’ mode can analyze IEIE or PIE with user defined amino acid residues. And also it can analyze PIEDA (pair interaction energy decomposition analysis). PIEDA decomposes total interaction energy to four components “ES/electro static”, “DS/dispersion”, “CT/charge transfer” and “EX/exchange”. It is useful to understand of details of the interaction so visualize these component is useful.

The authors showed two examples for the tool kit usage.
One is the case of BC2L-C. They conducted FMO between BC2L-C and seleno methylated fucose(SFU), and revealed new interaction that can not indicated as an interacting residue of SFU in the PDB record.

Understanding protein-ligand interaction is key for drug design so efficient analytical and visualization tools are important. The tool kit looks useful not only computational chemist but also medicinal chemist.

Advertisements