[3dem] CoVal: Mapping SARS-Cov2 genome mutations

[Joseph, Agnel Praveen (STFC,RAL,SC)]

Dear All,

We are happy to announce the first release of the CoVal database (https://urldefense.com/v3/__https://coval.ccpem.ac.uk__;!!Mih3wA!V8bym00oPyjOoTwpVcc0NrhoRysNwGQsJItKBy3ZYhAYTCnYVgHzLok28jKjLiQDAg$ <https://urldefense.com/v3/__https://coval.ccpem.ac.uk/__;!!Mih3wA!V8bym00oPyjOoTwpVcc0NrhoRysNwGQsJItKBy3ZYhAYTCnYVgHzLok28jIO1IfLoA$ >). CoVal is a database designed to identify amino acid replacement mutations from the genomes of SARS-CoV2 virus and map them onto 3D atomic models derived from cryo-EM data. The database is updated bi-weekly with new genome sequences from GISAID (https://urldefense.com/v3/__https://www.gisaid.org/__;!!Mih3wA!V8bym00oPyjOoTwpVcc0NrhoRysNwGQsJItKBy3ZYhAYTCnYVgHzLok28jKn1dfNGA$ ) and new depositions from PDB/EMDB. In the present release,11838 amino acid replacement mutations from 190696 genome sequences from GISAID (https://urldefense.com/v3/__https://www.gisaid.org/__;!!Mih3wA!V8bym00oPyjOoTwpVcc0NrhoRysNwGQsJItKBy3ZYhAYTCnYVgHzLok28jKn1dfNGA$ ) are included.The database also provides details on the demographic distribution of mutations and mapping the identified mutations onto the three-dimensional structures of proteins in various biological forms, determined experimentally using cryo-EM. CoVal is under active development and testing, and more features will be added in near future. The service will also be made available via CCP4-online: https://urldefense.com/v3/__https://ccp4online.ccp4.ac.uk/ccp4online/__;!!Mih3wA!V8bym00oPyjOoTwpVcc0NrhoRysNwGQsJItKBy3ZYhAYTCnYVgHzLok28jJH5nYI3Q$ .

One of the main aims behind development of this database is to provide various validation scores for global quality of the atomic models, and the local quality of mutation site(s) and the structural neighbors. This is highlighted using different quality indicators that are part of the CCP-EM software suite. We hope this service hosted by CCP-EM (STFC) is timely and beneficial to understand the impacts of mutations on protein structure and function, and also addresses the need of validation of cryo-EM derived structures. We plan to extend the database with structures derived from X-ray crystallography and also include insights on selected mutations based on molecular dynamics studies.
We hope the community will benefit from the resource and in case of any questions, please contact us for more details.

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