ArticleNucleic acids research2022
SCoV2-MD: a database for the dynamics of the SARS-CoV-2 proteome and variant impact predictions.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
22 citing papers in PubMed, 29 citations in OpenAlex.
- A dataset of small protein conformational ensembles from all-atom molecular dynamics simulations.Scientific data · 2026Article
- DynaRepo: the repository of macromolecular conformational dynamics.Nucleic acids research · 2026Article
- Beyond static structures: protein dynamic conformations modeling in the post-AlphaFold era.Briefings in bioinformatics · 2025Review
- VITALdb: to select the best viroinformatics tools for a desired virus or application.Briefings in bioinformatics · 2025Article
- Article
- mdCATH: A Large-Scale MD Dataset for Data-Driven Computational Biophysics.Scientific data · 2024Article
- COVID-AMD database for coronavirus-infected animal models with comparative analysis tools.Scientific reports · 2024Article
- Inhibition of the SARS-CoV-2 Non-structural Protein 5 (NSP5) Protease by Nitrosocarbonyl-Bases Small Molecules.ACS omega · 2024Article
- ThermoPCD: a database of molecular dynamics trajectories of antibody-antigen complexes at physiologic and fever-range temperatures.Database : the journal of biological databases and curation · 2024Article
- ATLAS: protein flexibility description from atomistic molecular dynamics simulations.Nucleic acids research · 2024Article
- A new paradigm for molecular dynamics databases: the COVID-19 database, the legacy of a titanic community effort.Nucleic acids research · 2024Article
- Deciphering dengue: novel RNA barcoding segments for enhanced serotype-specific identification and global surveillance of dengue viruses.Frontiers in microbiology · 2024Article
- Insights from incorporating quantum computing into drug design workflows.Bioinformatics (Oxford, England) · 2023Article
- Applying the digital data and the bioinformatics tools in SARS-CoV-2 research.Computational and structural biotechnology journal · 2023Review
- CoVEffect: interactive system for mining the effects of SARS-CoV-2 mutations and variants based on deep learning.GigaScience · 2022Article
- Biochemical Characterization of Emerging SARS-CoV-2 Nsp15 Endoribonuclease Variants.Journal of molecular biology · 2022Article
- Predicting COVID-19 disease severity from SARS-CoV-2 spike protein sequence by mixed effects machine learning.Computers in biology and medicine · 2022Article
- Biochemical Characterization of Emerging SARS-CoV-2 Nsp15 Endoribonuclease Variants.bioRxiv : the preprint server for biology · 2022Article
- Potential Resistance of SARS-CoV-2 Main Protease (Mpro) against Protease Inhibitors: Lessons Learned from HIV-1 Protease.International journal of molecular sciences · 2022Review
- The 2022 Nucleic Acids Research database issue and the online molecular biology database collection.Nucleic acids research · 2022Article
Corrections and comments
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Authors and funding
6 authors at 4 institutions in 3 countries.
Funding
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.
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What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.