ArticleThe international journal of high performance computing applications2021
AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics.
Article in The international journal of high performance computing applications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 82 papers.
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Who cites it
82 citing papers in PubMed, 177 citations in OpenAlex.
- Structural dynamics and allosteric communication of a SARS-like bat coronavirus spike glycoprotein.Biophysical journal · 2026Article
- SARS-CoV-2 Spike Protein's Structural Dynamics Affect the Activity of the Bebtelovimab Antibody.Journal of chemical information and modeling · 2026Article
- Deep learning insights into β-lactamase dynamics and resistance evolution.The Biochemical journal · 2026Review
- Condensate-Like Organization in Respiratory Aerosols Modulates the Dynamics of an Airborne Virus.bioRxiv : the preprint server for biology · 2026Article
- N-Glycans modulate tilting of HIV-1 envelope glycoprotein.Nature communications · 2026Article
- ReVesicle: Curation and Equilibration of Lipid Vesicles for Mesoscale Simulations.Journal of chemical theory and computation · 2026Article
- Interpretable machine learning uncovers structural determinants of Wnt-Wntless binding specificity from atomistic simulations.Communications chemistry · 2026Article
- The Open Molecular Software Foundation (OMSF) and the Growing Role of Open Source Software in Molecular Modeling.Journal of chemical information and modeling · 2026Review
- Beyond the Mutation Abyss: Revisiting SARS-CoV-2 Receptor-Binding Domain Evolution from ACE2 Binding Optimization to Immune Epitope Remodeling.Pathogens (Basel, Switzerland) · 2026Article
- Efficient sampling of large-scale transition pathways and intermediate conformations in sub-mesoscopic protein complexes.Nature communications · 2026Article
- Advanced Computational Methods in Protein Simulations: A Case Study of Enhanced Sampling Applied to Membrane Transporters.Advances in experimental medicine and biology · 2026Review
- Enhanced Sampling and Free Energy Calculations in Protein Simulations.Advances in experimental medicine and biology · 2026Review
- Polymyxins slow down lateral diffusion of proteins and lipopolysaccharide in the E. coli outer membrane.Communications biology · 2025Article
- Weighted Ensemble Simulations With the Drude Polarizable Model.Journal of computational chemistry · 2025Article
- Computationally designed mRNA-launched protein nanoparticle immunogens elicit protective antibody and T cell responses in mice.Science translational medicine · 2025Article
- Molecular dynamics simulations of biological membranes and membrane-associated phenomena across scales.Current opinion in structural biology · 2025Review
- Atomistic simulations of intact virus capsids: A computational challenge worth the scientific payoff.Current opinion in structural biology · 2025Review
- GPU Accelerated Hybrid Particle-Field Molecular Dynamics: Multi-Node/Multi-GPU Implementation and Large-Scale Benchmarks of the OCCAM Code.Journal of computational chemistry · 2025Article
- Article
- Unsupervised Learning of Progress Coordinates during Weighted Ensemble Simulations: Application to NTL9 Protein Folding.Journal of chemical theory and computation · 2025Article
22 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
29 authors at 10 institutions in 2 countries.
Funding
Abstract
We develop a generalizable AI-driven workflow that leverages heterogeneous HPC resources to explore the time-dependent dynamics of molecular systems. We use this workflow to investigate the mechanisms of infectivity of the SARS-CoV-2 spike protein, the main viral infection machinery. Our workflow enables more efficient investigation of spike dynamics in a variety of complex environments, including within a complete SARS-CoV-2 viral envelope simulation, which contains 305 million atoms and shows strong scaling on ORNL Summit using NAMD. We present several novel scientific discoveries, including the elucidation of the spike's full glycan shield, the role of spike glycans in modulating the infectivity of the virus, and the characterization of the flexible interactions between the spike and the human ACE2 receptor. We also demonstrate how AI can accelerate conformational sampling across different systems and pave the way for the future application of such methods to additional studies in SARS-CoV-2 and other molecular systems.
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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.