R. Podgornik

Evolutionary changes in the number of dissociable amino acids on spike proteins and nucleoproteins of SARS-CoV-2 variants

The paper analyzes the evolutionary changes in dissociable amino acids on SARS-CoV-2 spike and nucleoproteins, finding increased positive charge on spike proteins up to Omicron but not beyond, and no similar trend in nucleocapsid proteins.

Impact of BA.1, BA.2, and BA.4/BA.5 Omicron Mutations on Therapeutic Monoclonal Antibodies

This study uses molecular dynamics simulations to assess how Omicron subvariant mutations affect binding to therapeutic monoclonal antibodies, finding significant loss of activity for most mAbs.

Effect of Delta and Omicron mutations on the RBD-SD1 do-main of the Spike protein in SARS-CoV-2 and the Omicron mutations on RBD-ACE2 interface complex

This study uses DFT-based computational analysis to examine how Delta and Omicron mutations affect the RBD-SD1 domain and RBD-ACE2 interface of SARS-CoV-2, revealing structural and interaction changes linked to increased infectivity.

Atomic-scale Quantum Chemical Calculation of Omicron Mutations Near Cleavage Sites of the Spike Protein

This study uses quantum chemical calculations to analyze Omicron mutations near SARS-CoV-2 cleavage sites, identifying structural and electronic changes that may affect viral function.

Binding Interactions between RBD of Spike-Protein and Human ACE2 in Omicron variant

This study uses molecular dynamics simulations to analyze how mutations in the Omicron variant's spike protein RBD affect ACE2 binding, showing increased efficiency and tighter binding due to electrostatic interactions.

Mutations of Omicron variant at the interface of the receptor domain motif and human angiotensin-converting enzyme-2

This study uses computational modeling to analyze Omicron variant mutations at the spike protein-ACE2 interface, showing structural and charge changes that enhance binding strength.

Delta variant with P681R critical mutation revealed by ultra-large atomic-scale ab initio simulation: Implications for the fundamentals of biomolecular interactions

The paper uses ab initio simulations to analyze the P681R and D614G mutations in the SARS-CoV-2 spike protein, showing they reduce atomic bonding cohesion and increase flexibility, potentially aiding in predicting future mutations.

RNA secondary structure regulates fragments' adsorption onto flat substrates

This study investigates how RNA secondary structures affect adsorption onto flat substrates using multiscale simulations and identifies a dual adsorption regime based on surface interaction strength.