In an effort to help in the battle against COVID-19, the team at Iff Technologies has used our quantum algorithm for protiein binding site modeling to come up with the binding sites that exist within the interaction complex that exists between the SARS-COV-2 virus spike (S) protein and the ACE2 enzyme that helps in blood flow circulation.
Within this repository you will find:
sanitized_6lzg.pdb -> This is a pdb file of the atoms related to the top binding sites of the spike-ACE2 complex. This can help in narrowing down the total number of binding targets and for analysis methods with molecular analysis software, such as OVITO.
sanitized_6lzg.pdbqt -> This is a pdbqt file of the atoms related to the top binding sites of the spike-ACE2 complex. This is the file needed for docking tests using Autodock Vina.
Azithromycin.pdbqt -> PDBQT version of the Azithromycin pdb file for use in Autodock Vina.
Hydroxychloroquine.pdbqt -> PDBQT version of the Hydrochloroquine pdb file for use in Audoock Vina.
azithromycinae2spikepolarplus.pdbqt -> Binding conformations obtained from Autodock Vina for the spike-ACE2 complex and Azithromycin. Can be viewed in Python Molecule Viewer.
hydroxychloroquinespikeae2polarplus.pdbqt -> Binding conformations obtained from Autodock Vina for the spike-ACE2 complex and Hydroxychloroquine. Can be viewed in Python Molecule Viewer.
confcoronavirus.txt -> Config file for Autodock Vina docking of the spike-receptor complex. The coordinates do not need to be changed when switching ligand files.