Month: June 2020

Calculating the change in Gibbs free energy (ddGbind) of inhibitor binding associated with genetic variations of SARS-CoV-2 Main Protease – Post 4

Posted onAuthorSetayesh YazdaniLeave a comment

In my last post, I briefly mentioned our work in collaboration with Nicola de Maio from Nick Goldman’s lab, at EMBL’s European Bioinformatics Institute (EBI). What Nicola is doing is filtering out unreliable sequences of SARS-CoV-2 samples before analyzing them for genetic variability at the drug-binding sites of SARS-CoV-2 proteins that we want to investigate. First, Read More …

UBE3A Wnt signaling Cell Assay

Posted onAuthorVictoria VuLeave a comment

Background Apart from my HTT protein project, I also work on UBE3A, a HECT domain E3 ligase. E3 ligases work as a part of the ubiquitination system interacting with E2 ubiquitin-conjugating enzymes to transfer ubiquitin onto target substrate proteins. Ubiquitination of substrate proteins regulate a diversity of cell processes and is also important for ubiquitin-mediated Read More …

Genetic diversity at the catalytic site of the main SARS-CoV-2 protease

Posted onAuthorNicola De MaioLeave a comment

We investigated genetic variation of SARS-CoV-2 at the catalytic site of the main SARS-CoV-2 protease, following the work of Setayesh Yazdani (see https://zenodo.org/record/3834875#.Xs1IHsZ7nyk and https://openlabnotebooks.org/mapping-the-genetic-variations-of-sars-cov-2-onto-its-proteins-crystal-structures-post-1/ ). We collected information from more than 15,000 genomic sequences available from GISAID (https://www.epicov.org/) available on the 17th of May 2020, givig us considerable power to detect viral genetic variation Read More …