This is a preliminary web page with in-progress content.
We are using in silico modelling of SARS-CoV-2 drug targets, i.e. SARS-CoV-2 protein structures as deposited on the Protein Databank, to study the flexibility, rigidity and mobility of said proteins. This is generally an important step in trying to ascertain the dynamics of proteins for further drug-related docking studies (where people try to see if certain molecules, such as antivirals, can attach/dock to said proteins and hence interrupt their usual working).
Often, and certainly depending on the size and complexity of a given protein structure, state-of-the-art molecular dynamics studies of protein dynamics can take weeks and months, while our method only takes minutes to hours. Although the physical/biological basis for the method is less sophisticated, the results should be able to offer a good first guess on the possible protein dynamics and hence allow to circumvent lengthy MD studies. Due to the speed of the method, large-scale screening (of all thus far published SARS-CoV-2 protein structures in the PDB!) is possible.
We have now completed this study for 134 such protein structures (available by April 18th) and are currently extending the study to the remaining 175-134 = 41 additional structures that became available by May 19th.
Links to further information
- pdb2movie scripts
- Paper draft (to allow quick dissemination)
- WPRN network listing
- SharePoint site for team members
Questions? Leave us comments/questions/suggestions at @pdb2movie