A. Sofia F. Oliveira

This study uses D-NEMD simulations to show how cancer mutations in EGFR alter allosteric communication networks and signal propagation within the kinase domain.

This paper introduces a D-NEMD method to identify allosteric positions in proteins by analyzing long-range structural responses to alanine substitutions, validated on KPC-2 beta-lactamase.

This study uses D-NEMD simulations to show how pH changes induce variant-specific conformational changes in SARS-CoV-2 spike proteins, affecting their stability and entry mechanisms.

This paper identifies critical receptor-ligand interactions that distinguish varenicline from other nAChR agonists, revealing unique hydrogen bonding interactions essential for its function.

This paper uses D-NEMD simulations to study how the fatty acid site in the glycosylated SARS-CoV-2 spike modulates its structure and function, revealing allosteric networks and the role of glycans.

This study uses de novo protein design to investigate redox cooperativity in multiheme cytochromes, showing that membrane burial enhances heme-heme electrostatic coupling.

The paper uses dynamical simulations and experiments to identify a distal site in an antibiotic resistance enzyme that modulates activity when mutated.

This study uses dynamical nonequilibrium molecular dynamics simulations to investigate how SARS-CoV-2 main protease dynamically recognizes and responds to substrate binding, revealing key conformational changes and substrate selectivity mechanisms.

This study investigates how the BriS{Delta} variant of SARS-CoV-2 affects spike structure, function, and infectivity across different cell types.

The paper designs and validates de novo proteins with single and multi-heme binding capabilities, achieving atomic-level structural resolution for functional engineering.

The paper investigates how CHRNA5-A3-B4 gene variants affect smoking behaviors and nicotine responses in humans, finding reduced cravings and smoke inhalation in minor allele carriers.