COVID (SARS CoV-2) Downloads
This is a theoretically derived homology model of SARs CoV-2's nsp12 replicase made from the sequence of; R1AB_WCPV Replicase polyprotein 1ab (R1ab) available at: https://viralzone.expasy.org/8996
I used Protein data Bank entry " 6nur.pdb " chain A, a structure of SAR-CoV's ns12 replicase as a template (1).
I made this homology model, out of interest, with Bioinfomatics Toolkit (https://toolkit.tuebingen.mpg.de/), toward the end of my last academic position (2).
(1) Structure of the SARS-CoV nsp12 polymerase bound to nsp7 and nsp8 co-factors. Kirchdoerfer, R.N., Ward, A.B. (2019) Nat Commun 10: 2342-2342, PubMed: 31138817 Search on PubMed, DOI: 10.1038/s41467-019-10280-3(2) A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core. Zimmermann L, Stephens A, Nam SZ, Rau D, Kübler J, Lozajic M, Gabler F, Söding J, Lupas AN, Alva V. J Mol Biol. 2018 Jul 20. S0022-2836(17)30587-9.
Virtual Screening for potentially inhibitory compounds is currently underway, using this model. Please email email@example.com for collaboration and data sharing. In advance of your contact; THANK YOU!!!
SARS CoV-2 nsp12 Replicase homology model
4/7/2020 UPDATE on currently available data... A different group, Gao et al., has solved a Cryo-EM structure available in the Protein Data Bank as of early April. The link is:
A structural alignment of FSDP's homology model vs Gao et al.'s ns12 (yellow) is shown at right. FSDP's model was extremely close. Root mean square deviation (RSMD) of ~ 0.66 angstroms as calculated by DEEPVIEW.
Virtual screening is progressing...
A newer structure is available form GAO et al...