SCoV2-MD: a database for the dynamics of the SARS-CoV-2 proteome and variant impact predictions

Mariona Torrens-Fontanals, Alejandro Peralta-García, Carmine Talarico, Ramon Guixà-González, Toni Giorgino, and Jana Selent

Nucleic Acids Research (2022) 50 (D1), D858–D866, doi:10.1093/nar/gkab977

SCoV2-MD is a new online resource that systematically organizes atomistic simulations of the SARS-CoV-2 proteome. The database includes simulations produced by leading groups using molecular dynamics (MD) methods to investigate the structure-dynamics-function relationships of viral proteins. SCoV2-MD cross-references the molecular data with the pandemic evolution by tracking all available variants sequenced during the pandemic and deposited in the GISAID resource. SCoV2-MD enables the interactive analysis of the deposited trajectories through a web interface, which enables users to search by viral protein, isolate, phylogenetic attributes, or specific point mutation. Each mutation can then be analyzed interactively combining static (e.g. a variety of amino acid substitution penalties) and dynamic (time-dependent data derived from the dynamics of the local geometry) scores.

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