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Examining Functional Linkages Between Conformational Dynamics, Protein Stability and Evolution of Cryptic Binding Pockets in the SARS-CoV-2 Omicron Spike Complexes with the ACE2 Host Receptor: Recombinant Omicron Variants Mediate Variability of Conserved Allosteric Sites and Binding Epitopes

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Fast procedure for reconstruction of full‐atom protein models from reduced representations
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Deep Mutational Scanning of SARS-CoV-2 Receptor Binding Domain Reveals Constraints on Folding and ACE2 Binding
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Structural and functional characterizations of infectivity and immune evasion of SARS-CoV-2 Omicron
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Structural basis of human ACE2 higher binding affinity to currently circulating Omicron SARS-CoV-2 sub-variants BA.2 and BA.1.1
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Cryo-EM structure of the SARS-CoV-2 Omicron spike
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Structures of Omicron spike complexes and implications for neutralizing antibody development
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Inter-domain communication in SARS-CoV-2 spike proteins controls protease-triggered cell entry
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Cryo-EM structures of SARS-CoV-2 Omicron BA.2 spike
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A delicate balance between antibody evasion and ACE2 affinity for Omicron BA.2.75
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Real-Time Conformational Dynamics of SARS-CoV-2 Spikes on Virus Particles
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Antigenic characterization of the SARS-CoV-2 Omicron subvariant BA.2.75
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Evasion of neutralizing antibody responses by the SARS-CoV-2 BA.2.75 variant
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Characterization of the enhanced infectivity and antibody evasion of Omicron BA.2.75
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Virological characteristics of the SARS-CoV-2 Omicron BA.2.75 variant
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Identifying promising druggable binding sites and their flexibility to target the receptor-binding domain of SARS-CoV-2 spike protein
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Structural Diversity of the SARS-CoV-2 Omicron Spike
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Uncovering cryptic pockets in the SARS-CoV-2 spike glycoprotein
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Using generalized ensemble simulations and Markov state models to identify conformational states
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ACE2 binding and antibody evasion in enhanced transmissibility of XBB.1.5
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Comparative Perturbation-Based Modeling of the SARS-CoV-2 Spike Protein Binding with Host Receptor and Neutralizing Antibodies: Structurally Adaptable Allosteric Communication Hotspots Define Spike Sites Targeted by Global Circulating Mutations
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Dynamic Profiling of Binding and Allosteric Propensities of the SARS-CoV-2 Spike Protein with Different Classes of Antibodies: Mutational and Perturbation-Based Scanning Reveals the Allosteric Duality of Functionally Adaptable Hotspots
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A Stochastic Algorithm for the Isobaric–Isothermal Ensemble with Ewald Summations for All Long Range Forces
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Accurate Estimation of Protein Folding and Unfolding Times: Beyond Markov State Models
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tICA-Metadynamics: Accelerating Metadynamics by Using Kinetically Selected Collective Variables
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Probing the Allosteric Inhibition Mechanism of a Spike Protein Using Molecular Dynamics Simulations and Active Compound Identifications
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Dynamic Network Modeling of Allosteric Interactions and Communication Pathways in the SARS-CoV-2 Spike Trimer Mutants: Differential Modulation of Conformational Landscapes and Signal Transmission via Cascades of Regulatory Switches
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Integrated Biophysical Modeling of the SARS-CoV-2 Spike Protein Binding and Allosteric Interactions with Antibodies
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UMAP as a Dimensionality Reduction Tool for Molecular Dynamics Simulations of Biomacromolecules: A Comparison Study
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Validating Molecular Dynamics Simulations against Experimental Observables in Light of Underlying Conformational Ensembles
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hACE2-Induced Allosteric Activation in SARS-CoV versus SARS-CoV-2 Spike Assemblies Revealed by Structural Dynamics
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PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical p K a Predictions
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Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of p K a Values
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Improvements in Markov State Model Construction Reveal Many Non-Native Interactions in the Folding of NTL9
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CHARMM36m: an improved force field for folded and intrinsically disordered proteins
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Characterization of SARS-CoV-2 Omicron spike RBD reveals significantly decreased stability, severe evasion of neutralizing-antibody recognition but unaffected engagement by decoy ACE2 modified for enhanced RBD binding
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Targetable elements in SARS-CoV-2 S2 subunit for the design of pan-coronavirus fusion inhibitors and vaccines
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Defining a highly conserved cryptic epitope for antibody recognition of SARS-CoV-2 variants
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Structural and biochemical mechanism for increased infectivity and immune evasion of Omicron BA.2 variant compared to BA.1 and their possible mouse origins
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Profound neutralization evasion and augmented host cell entry are hallmarks of the fast-spreading SARS-CoV-2 lineage XBB.1.5
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Structural and biochemical rationale for enhanced spike protein fitness in delta and kappa SARS-CoV-2 variants
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Cryo-EM structure of a SARS-CoV-2 omicron spike protein ectodomain
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Structural dynamics in the evolution of SARS-CoV-2 spike glycoprotein
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Virological characteristics of the SARS-CoV-2 XBB variant derived from recombination of two Omicron subvariants
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Structural basis for receptor binding and broader interspecies receptor recognition of currently circulating Omicron sub-variants
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SARS-CoV-2 simulations go exascale to predict dramatic spike opening and cryptic pockets across the proteome
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Receptor binding and priming of the spike protein of SARS-CoV-2 for membrane fusion
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Molecular basis of receptor binding and antibody neutralization of Omicron
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BA.2.12.1, BA.4 and BA.5 escape antibodies elicited by Omicron infection
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Imprinted SARS-CoV-2 humoral immunity induces convergent Omicron RBD evolution
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Controlling the SARS-CoV-2 spike glycoprotein conformation
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The SARS-CoV-2 spike reversibly samples an open-trimer conformation exposing novel epitopes
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Structural and functional characteristics of the SARS-CoV-2 Omicron subvariant BA.2 spike protein
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Brownian dynamics simulation of a lipid chain in a membrane bilayer
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Estimation and uncertainty of reversible Markov models
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Discovery of multiple hidden allosteric sites by combining Markov state models and experiments
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A Fast 3 × N Matrix Multiply Routine for Calculation of Protein RMSD
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Cryo-EM reveals binding of linoleic acid to SARS-CoV-2 spike glycoprotein, suggesting an antiviral treatment strategy
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Conformational dynamics of SARS-CoV-2 trimeric spike glycoprotein in complex with receptor ACE2 revealed by cryo-EM
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Cryo-electron Microscopy Structure of S-Trimer, a Subunit Vaccine Candidate for COVID-19
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Structure of a Vaccine-Induced, Germline-Encoded Human Antibody Defines a Neutralizing Epitope on the SARS-CoV-2 Spike N-Terminal Domain
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Deep mutational scans for ACE2 binding, RBD expression, and antibody escape in the SARS-CoV-2 Omicron BA.1 and BA.2 receptor-binding domains
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