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SARS-CoV-2 Simulations Go Exascale to Capture Spike Opening and Reveal Cryptic Pockets Across the Proteome

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Outgoing claims: the papers this work cites, builds on, or argues with.

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Case-Fatality Rate and Characteristics of Patients Dying in Relation to COVID-19 in Italy
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MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories
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A cryptic pocket in Ebola VP35 allosterically controls RNA binding
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Electron Cryo-microscopy Structure of Ebola Virus Nucleoprotein Reveals a Mechanism for Nucleocapsid-like Assembly
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SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor
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Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein
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Neutralization of SARS-CoV-2 by Destruction of the Prefusion Spike
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Neutralization of SARS-CoV-2 by Destruction of the Prefusion Spike
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GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers
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CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field
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P-LINCS: A Parallel Linear Constraint Solver for Molecular Simulation
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Molecular Simulation of ab Initio Protein Folding for a Millisecond Folder NTL9(1−39)
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Markov State Models: From an Art to a Science
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Enspara : Modeling molecular ensembles with scalable data structures and parallel computing
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Crystal structure of NL63 respiratory coronavirus receptor-binding domain complexed with its human receptor
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Cell entry mechanisms of SARS-CoV-2
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The reproductive number of COVID-19 is higher compared to SARS coronavirus
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MUSCLE: multiple sequence alignment with high accuracy and high throughput
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UniProt: a worldwide hub of protein knowledge
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SWISS-MODEL: homology modelling of protein structures and complexes
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Map of SARS-CoV-2 spike epitopes not shielded by glycans
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Cryo-EM Structures Delineate a pH-Dependent Switch that Mediates Endosomal Positioning of SARS-CoV-2 Spike Receptor-Binding Domains
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How Fast-Folding Proteins Fold
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Screen Savers of the World Unite!
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Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation
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Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors
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Potent neutralizing antibodies from COVID-19 patients define multiple targets of vulnerability
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Studies in humanized mice and convalescent humans yield a SARS-CoV-2 antibody cocktail
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In situ structural analysis of SARS-CoV-2 spike reveals flexibility mediated by three hinges
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Coronavirus: covid-19 has killed more people than SARS and MERS combined, despite lower case fatality rate
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Structure-Based Vaccine Antigen Design
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OpenMM 7: Rapid development of high performance algorithms for molecular dynamics
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Designing small molecules to target cryptic pockets yields both positive and negative allosteric modulators
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Structural basis of RNA recognition by the SARS-CoV-2 nucleocapsid phosphoprotein
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Why Does COVID-19 Case Fatality Rate Vary Among Countries?
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Neutralization of SARS-CoV-2 by Destruction of the Prefusion Spike
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Cross-Country Comparison of Case Fatality Rates of COVID-19/SARS-COV-2
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Molecular Docking and Structure-Based Drug Design Strategies
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The Coronavirus Nucleocapsid Is a Multifunctional Protein
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Simulation of spontaneous G protein activation reveals a new intermediate driving GDP unbinding
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The dynamic conformational landscape of the protein methyltransferase SETD8
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Conformational distributions of isolated myosin motor domains encode their mechanochemical properties

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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