R. E. Amaro

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 designs stabilized SARS-CoV-2 S2 immunogens using simulation-driven approaches, showing improved stability and immunogenicity.

The paper identifies SARS-CoV-2 variants resistant to protease inhibitors nirmatrelvir and ensitrelvir, showing pre-existing resistance and potential for spread.

The paper uses a mucinase to analyze glycoproteomic features of TIM family proteins and shows how glycosylation affects their structure through molecular dynamics simulations.

The paper ranks JAK2/STAT5 inhibitors based on kinetic properties using MMVT in SEEKR2 to explain their selectivity over JAK3.

This study uses mesoscale simulations to analyze the dynamics of influenza glycoproteins, revealing new antigenic states and a vulnerability site in neuraminidase.

This study develops a first-in-class Aurora-A/N-Myc degrader, HLB-0532259, which effectively reduces N-Myc levels and shows tumor reduction in neuroblastoma models.

This paper develops aminoadamantane nitrate compounds that inhibit SARS-CoV-2 infection by S-nitrosylating ACE2 and blocking viral entry, showing efficacy in vitro and in a Syrian hamster model.

The paper identifies chimallin as the primary protein forming the bacteriophage nuclear shell and characterizes its self-assembly into closed compartments.

The paper identifies cryptic and allosteric pockets in the SARS-CoV-2 main protease using enhanced sampling methods and assesses their druggability for potential inhibitor development.

This study identifies the mechanism by which derlin rhomboid pseudoproteases facilitate retrotranslocation of ER membrane substrates through substrate engagement and lipid thinning.

This study determines the structure of SARS-CoV-2 ExoN and its interaction with nsp10, revealing mechanisms of RNA substrate binding and exoribonuclease activity.

This paper introduces Independent Markov Decomposition (IMD) to model kinetics of biomolecular complexes by decomposing systems into weakly coupled subsystems, reducing sampling requirements while preserving accuracy.

This study identifies a glycan gate and key residues that facilitate SARS-CoV-2 spike protein RBD opening through simulations and experimental validation.

This paper identifies a novel allosteric site on IKK2 that can be targeted by small-molecule inhibitors to block its activity without ATP-competitive off-target effects.

This study shows that three mutations in SARS-CoV-2 allowed it to escape neutralization by a highly neutralizing convalescent plasma.

This study investigates how mutations in PI3Kγ affect its regulatory dynamics and identifies a strategy for developing selective inhibitors.

This paper develops an AI-driven workflow to simulate SARS-CoV-2 spike protein dynamics, revealing glycan shield structure, spike glycans' role in infectivity, and spike-ACE2 interactions.

The paper uses Markov state models and NMR to study p53 mutations, revealing a previously overlooked allosteric loop involved in conformational dynamics and mutation-induced inactivation.

This paper develops a multiscale coarse-grained model of the SARS-CoV-2 virion using structural data and all-atom simulations to enable large-scale viral process simulations.

High school students benchmarked ensemble docking methods for ligand affinity prediction in a drug discovery challenge, finding Cathepsin S challenging and exploring advanced techniques.

This paper uses molecular dynamics simulations to study ACE2 flexibility in SARS-CoV-2 infection, finding structural dynamics that may aid viral entry and therapeutic design.

This study uses multiscale simulations to show glycans reduce drug binding to influenza neuraminidase by sterically blocking the primary binding site.

The paper uses molecular simulations to show that the SARS-CoV-2 spike protein's Y674-R685 loop binds to nicotinic acetylcholine receptors, with specific interactions and conformational changes observed across different receptor subtypes.

This study reveals the structural role of glycans in modulating SARS-CoV-2 spike protein conformational dynamics and ACE2 binding through molecular simulations and experiments.

The paper introduces GAMer 2, a mesh generation tool for converting structural biology data into geometric meshes suitable for biophysical modeling.

This study reports structures of APOBEC3B with loop 7 from APOBEC3G, revealing inactive conformations stabilized by small molecules, providing insights for inhibitor design.

This study investigates how orthosteric and allosteric antagonists affect CCR2 dynamics using molecular dynamics simulations and Markov-state models, revealing stable inactive conformations and potential drug binding sites.