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

Abstract

SCoV2-MD (www.scov2-md.org) 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. Dynamic scores can be computed on the basis of nine non-covalent interaction types, including steric properties, solvent accessibility, hydrogen bonding, and other types of chemical interactions. Where available, experimental data such as antibody escape and change in binding affinities from deep mutational scanning experiments are also made available. All metrics can be combined to build predefined or custom scores to interrogate the impact of evolving variants on protein structure and function.

Potential Resistance of SARS-CoV-2 Main Protease (Mpro) against Protease Inhibitors: Lessons Learned from HIV-1 Protease

“…The SARS-CoV-2 genome sequences are available through databases, such as the Global Initiative on Sharing All Influenza Data (GISAID) [ 88 ] and NCBI databases, and additional databases are also available that can aid variant analysis, including COVID-3D online resource [ 89 ], SCoV2-MD [ 90 ], and SARS-CoV-2 3D [ 91 ]. For this review, we obtained data about SARS-CoV-2 variants from the COVID-3D online resource ( , accessed on 20 February 2022) [ 89 ].…”

The 2022Nucleic Acids Researchdatabase issue and the online molecular biology database collection

“…The COVID-19 papers include the SCoV2-MD publication ( 4 ) that is the first ‘Breakthrough’ Article in the Issue. NAR assigns Breakthrough status to papers that solve long-standing problems, or which are otherwise considered of exceptional importance.…”

Entrectinib—A SARS-CoV-2 Inhibitor in Human Lung Tissue (HLT) Cells

“…Both proteins were obtained, in an unbound state, from a simulation from D.E. Shaw's laboratory (Simulation ID: DESRES-ANTON-10895671 [32], based on PDB ID 6VW1, replicate 000151, first frame), also available in SCoV2-MD [42]. Then, the docking was performed against the RBD and ACE2, using the previously created database (see Section 4.2 (Database Creation)).…”