ArticlePLoS computational biology2021
Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants.
Article in PLoS computational biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
65 citing papers in PubMed.
- Molecular docking and dynamic simulation of marine natural products from soft coral-derived microbes against SARS-CoV-2 main protease and spike protein.Scientific reports · 2026Article
- Exploring the Intrinsic Structural Plasticity and Conformational Dynamics of Human Beta Coronavirus Spike Glycoproteins.Journal of chemical information and modeling · 2025Article
- Predicting pathogen evolution and immune evasion in the age of artificial intelligence.Computational and structural biotechnology journal · 2025Review
- Comprehensive analysis of SARS-CoV-2 Spike evolution: epitope classification and immune escape prediction.Virus evolution · 2025Article
- NRGSuite-Qt: a PyMOL plugin for high-throughput virtual screening, molecular docking, normal-mode analysis, the study of molecular interactions, and the detection of binding-site similarities.Bioinformatics advances · 2025Article
- COVID-19 mutations: An overview.World journal of methodology · 2024Review
- Article
- Raman Fingerprints of SARS-CoV-2 Omicron Subvariants: Molecular Roots of Virological Characteristics and Evolutionary Directions.ACS infectious diseases · 2023Article
- Protein conformational ensembles in function: roles and mechanisms.RSC chemical biology · 2023Review
- The DynaSig-ML Python package: automated learning of biomolecular dynamics-function relationships.Bioinformatics (Oxford, England) · 2023Article
- Article
- Interspecies transmission of SARS CoV-2 with special emphasis on viral mutations and ACE-2 receptor homology roles.International journal of veterinary science and medicine · 2023Review
- The diverse role of heparan sulfate and other GAGs in SARS-CoV-2 infections and therapeutics.Carbohydrate polymers · 2023Review
- A Modified Recombinant DNA-Based SARS-CoV-2 Vaccine Expressing Stabilized Uncleavable Spike Protein Elicits Humoral and Cellular Immunity against Various SARS-CoV-2 Variants of Concern.Transboundary and emerging diseases · 2023Article
- Evaluating the effect of SARS-CoV-2 spike mutations with a linear doubly robust learner.Frontiers in cellular and infection microbiology · 2023Article
- Force-tuned avidity of spike variant-ACE2 interactions viewed on the single-molecule level.Nature communications · 2022Article
- Sequence-sensitive elastic network captures dynamical features necessary for miR-125a maturation.PLoS computational biology · 2022Article
- Novel coronavirus mutations: Vaccine development and challenges.Microbial pathogenesis · 2022Review
- Probing the mutational landscape of the SARS-CoV-2 spike protein via quantum mechanical modeling of crystallographic structures.PNAS nexus · 2022Article
- Human coronaviruses: The emergence of SARS-CoV-2 and management of COVID-19.Virus research · 2022Review
5 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The SARS-CoV-2 Spike protein needs to be in an open-state conformation to interact with ACE2 to initiate viral entry. We utilise coarse-grained normal mode analysis to model the dynamics of Spike and calculate transition probabilities between states for 17081 variants including experimentally observed variants. Our results correctly model an increase in open-state occupancy for the more infectious D614G via an increase in flexibility of the closed-state and decrease of flexibility of the open-state. We predict the same effect for several mutations on glycine residues (404, 416, 504, 252) as well as residues K417, D467 and N501, including the N501Y mutation recently observed within the B.1.1.7, 501.V2 and P1 strains. This is, to our knowledge, the first use of normal mode analysis to model conformational state transitions and the effect of mutations on such transitions. The specific mutations of Spike identified here may guide future studies to increase our understanding of SARS-CoV-2 infection mechanisms and guide public health in their surveillance efforts.
Indexed as
Identifiers
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.