Physical Chemistry

Special feature of COVID-19 in FMODB: Fragment molecular orbital calculations and interaction energy analysis of SARS-CoV-2 related proteins

Authors

Abstract

SARS-CoV-2 is the causative agent of coronavirus, globally known as COVID-19. There are ongoing researches to develop effective therapeutics and vaccines against COVID-19 using various methods. We currently conduct research based on the fragment molecular orbital (FMO) method for calculating the electronic structure of protein complexes and analyzing their quantitative molecular interactions. This enables us to extensively analyze the molecular interactions in residues or functional group units acting inside protein complexes. Such precise interaction data are available in the FMO database (FMODB). We have performed several FMO calculations on the structures of SARS-CoV-2 related proteins registered in the protein data bank and published the results of 681 structures, including three structural proteins and eleven nonstructural proteins, on the COVID-19 special page.These data not only aid the interpretation of experimentally determined structures but also the understanding of protein functions, which is useful for rational drug design for COVID-19.

Content

Thumbnail image of FMODB-COVID-19-submitted.pdf

Supplementary material

Thumbnail image of FMODB-COVID-19-SI-submitted.pdf
Special feature of COVID-19 in FMODB: Fragment molecular orbital calculations and interaction energy analysis of SARS-CoV-2 related proteins
Supplementary Material for Special feature of COVID-19 in FMODB: Fragment molecular orbital calculations and interaction energy analysis of SARS-CoV-2 related proteins

Supplementary weblinks

FMO data for COVID-19-related proteins
We performed ab initio quantum chemical calculations based on the PDB structures using the FMO method and published the data at FMODB. We will continue to perform FMO calculations on the newly released PDB structures and update FMODB. The precise interaction data between the drug candidates and the proteins can be used for future drug design and vaccine development through FMODB.