ArticleNature chemistry2021
SARS-CoV-2 simulations go exascale to predict dramatic spike opening and cryptic pockets across the proteome.
Article in Nature chemistry, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 158 papers.
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Who cites it
158 citing papers in PubMed, 292 citations in OpenAlex.
- Disulfide bonds stabilize the SARS-CoV-2 RBD and preserve binding to ACE2 following thermal denaturation.Bioscience reports · 2026Article
- Hierarchical geometric deep learning enables scalable analysis of molecular dynamics.The Journal of chemical physics · 2026Article
- Flavonoids as Structural Probes Reveal Conformationally Dependent Ligand Recognition in the SARS-CoV-2 JN.1 Spike Protein.International journal of molecular sciences · 2026Article
- Eras of bioinformatics technologies from command-line interfaces to artificial intelligence (AI) chatbots.Briefings in bioinformatics · 2026Review
- Tyrosine kinases sample unique activation ensembles.bioRxiv : the preprint server for biology · 2026Article
- The Shape of Things to Come: α-Helical Membrane Protein Folding on the Ribosome.Chemical reviews · 2026Review
- Convergence is not correctness: context-dependent performance of enhanced-sampling methods across biological complexity.Nature communications · 2026Article
- Absolute Binding Free Energy Calculations between the SARS-CoV-2 Main Protease and 130 Drug Leads Using Implicit Ligand Theory.Journal of chemical information and modeling · 2026Article
- Mechanisms of Binding and Immune Escape Resistance for Broadly Neutralizing Antibodies Targeting Distinct Conserved SARS-CoV-2 Spike Epitopes: A Hierarchical Approach Integrating Mutational Profiling and Energy Landscape Analysis.International journal of molecular sciences · 2026Article
- Prefusion-stabilized SARS-CoV-2 spike reshapes antigenic hierarchy and antibody targeting against conserved and occluded epitopes.NPJ vaccines · 2026Article
- Frustration Landscapes of Broadly Neutralizing SARS-CoV-2 Spike Antibodies Targeting Conserved Epitopes Reveal Energetic Logic of Escape-Proof and Escape-Prone Mechanisms.bioRxiv : the preprint server for biology · 2026Article
- Fast sampling of protein conformational dynamics.Science advances · 2026Article
- Exploring the Structural Basis of Cryptic Pocket Formation Driven by Extensive Protein Conformational Changes in Drug Targets.Journal of chemical theory and computation · 2026Article
- Conformational dynamics of SARS-CoV-2 spike on a membrane reveals the allosteric effects of furin cleavage and the D614G mutation.Science advances · 2026Article
- The buried S2 apex of SARS-CoV-2 spike elicits an immunodominant germline-restricted public antibody response.bioRxiv : the preprint server for biology · 2026Article
- Decrypting cryptic pockets with physics-based simulations and artificial intelligence.Current opinion in structural biology · 2026Review
- Computational Ligand-Binding Site Prediction.Advances in experimental medicine and biology · 2026Review
- Common cold embecovirus imprinting primes broadly neutralizing antibody responses to SARS-CoV-2 S2.The Journal of experimental medicine · 2025Article
- Neutral Frustration Landscape Architecture of SARS-CoV-2 Spike-Antibody Interfaces Shapes Immune Evasion Mechanisms for Ultrapotent Neutralizing Antibodies and Determines Pathways of Viral Adaptation: Insights from Integrative Computational Approach.bioRxiv : the preprint server for biology · 2025Article
- Identification and understanding of allostery hotspots in proteins: Integration of deep mutational scanning and multi-faceted computational analyses.Journal of molecular biology · 2025Review
98 more citing papers are in PubMed but not listed here.
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Authors and funding
18 authors at 5 institutions in 2 countries.
Funding
Abstract
SARS-CoV-2 has intricate mechanisms for initiating infection, immune evasion/suppression and replication that depend on the structure and dynamics of its constituent proteins. Many protein structures have been solved, but far less is known about their relevant conformational changes. To address this challenge, over a million citizen scientists banded together through the Folding@home distributed computing project to create the first exascale computer and simulate 0.1 seconds of the viral proteome. Our adaptive sampling simulations predict dramatic opening of the apo spike complex, far beyond that seen experimentally, explaining and predicting the existence of 'cryptic' epitopes. Different spike variants modulate the probabilities of open versus closed structures, balancing receptor binding and immune evasion. We also discover dramatic conformational changes across the proteome, which reveal over 50 'cryptic' pockets that expand targeting options for the design of antivirals. All data and models are freely available online, providing a quantitative structural atlas.
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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.