S. Agajanian

Atomistic Simulations and Network-Based Energetic Profiling of Binding and Allostery in the SARS-CoV-2 Spike Omicron BA.1, BA.1.1, BA.2 and BA.3 Subvariant Complexes with the Host Receptor: Revealing Hidden Functional Roles of the Binding Hotspots in Mediating Epistatic Effects and Long-Range Communication with Allosteric Pockets

This study uses atomistic simulations and network analysis to quantify binding energy hotspots and epistatic effects in Omicron subvariant RBD-ACE2 complexes.

Integrating Conformational Dynamics and Perturbation-Based Network Modeling for Mutational Profiling of Binding and Allostery in the SARS-CoV-2 Spike Variant Complexes with Antibodies: Balancing Local and Global Determinants of Mutational Escape Mechanisms

This study integrates conformational dynamics and perturbation-based network modeling to analyze mutational escape mechanisms in SARS-CoV-2 spike variants bound to antibodies.

Hierarchical Computational Modeling and Dynamic Network Analysis of Allosteric Regulation in the SARS-CoV-2 Spike Omicron Trimer Structures: Omicron Mutations Cooperate to Allosterically Control Balance of Protein Stability and Conformational Adaptability

This study uses computational modeling to analyze how Omicron mutations in the SARS-CoV-2 spike protein regulate structural stability and conformational adaptability through allosteric networks.

The Landscape-Based Protein Stability Analysis and Network Modeling of Multiple Conformational States of the SARS-CoV-2 Spike D614 Mutant: Conformational Plasticity and Frustration-Driven Allostery as Energetic Drivers of Highly Transmissible Spike Variant

This study analyzes the conformational dynamics and mutational sensitivity of the SARS-CoV-2 D614G spike mutant using simulations and network analysis, finding increased conformational adaptability and allosteric regulation.

Atomistic Simulations and Deep Mutational Scanning of Protein Stability and Binding Interactions in the SARS-CoV-2 Spike Protein Complexes with Nanobodies: Molecular Determinants of Mutational Escape Mechanisms

Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating Variants

This study analyzes the functional effects of the D614G mutation in SARS-CoV-2 spike proteins using computational methods, revealing its role in enhancing infectivity through stability changes in residue interaction networks.

Dynamic Profiling of Binding and Allosteric Propensities of the SARS-CoV-2 Spike Protein with Different Classes of Antibodies: Mutational and Perturbation-Based Scanning Reveal Allosteric Duality of Functionally Adaptable Hotspots

This study uses atomistic simulations and mutational scanning to analyze how different antibodies affect the allosteric properties of SARS-CoV-2 spike protein residues, revealing how mutations at K417, E484, and N501 influence antibody resistance.

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

This study identifies structurally adaptable allosteric hotspots in the SARS-CoV-2 spike protein that are targeted by mutations and antibodies, showing their role in modulating binding affinity and stability.

Computational Analysis of Protein Stability and Allosteric Interaction Networks in Distinct Conformational Forms of the SARS-CoV-2 Spike D614G Mutant: Reconciling Functional Mechanisms through Allosteric Model of Spike Regulation

This study uses computational methods to analyze how the D614G mutation in SARS-CoV-2 spike protein affects stability and allosteric communication, showing it enhances infectivity through structural changes.