Rommie E. Amaro

This paper introduces LDDM, a generative model for drug design that produces synthetically accessible compounds validated experimentally for five protein targets.

seekrflow automates drug-target kinetic and thermodynamic predictions using a multiscale milestoning simulation pipeline, achieving accurate results with reduced manual intervention and computational cost.

This paper investigates how the D614G mutation in SARS-CoV-2 spike protein alters conformational dynamics and allosteric communication, leading to faster RBD opening and increased infectivity.

This study uses molecular dynamics simulations to show how respiratory aerosols create structured microenvironments that influence SARS-CoV-2 stability and spike dynamics.

This study uses molecular dynamics simulations to analyze how mutations in the SHC014-CoV spike protein affect its structural dynamics and allosteric communication, revealing mechanisms that enhance viral entry.

This study generates the first wild-type full-length p53 tetramer model bound to DNA and analyzes its conformational dynamics and mutations in cancer mutants.

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.

The paper identifies an unconventional HxD motif in coronaviruses that functions as a coatomer-binding signal, revealing alternative pathways for viral morphogenesis.

This paper uses molecular dynamics simulations and Markovian State Models to analyze CK1 conformational dynamics, revealing how the tau mutant alters substrate selectivity and affects circadian period.

This study uses molecular dynamics simulations to show that membrane association of cPLA2 triggers conformational changes that enable its activation and phospholipid hydrolysis.

The paper uses cryo-EM to visualize intermediate states of dynein activation pathway by analyzing structures of dynein and dynein-Lis1 bound to ATP.

This study uses molecular dynamics simulations to show that N-linked glycans at positions N88 and N611 modulate HIV-1 Env tilting motion in a membrane environment.

This study models the full-length APOBEC3B structure and finds that NTD-CTD interactions increase active site opening frequency.

This study compares the conformational dynamics of native SARS-CoV-2 Spike protein in virus-like particles to recombinant Spike, finding reduced dynamics in VLP S and implications for epitope display.

This study characterizes RHBDL4 enzymatic properties using an in vitro platform, identifying effective inhibitors and providing insights for drug development.

The paper investigates how SARS-like bat coronaviruses evolve enhanced receptor binding and cell entry through specific genetic substitutions.

The paper predicts drug residence times for threonine-tyrosine kinase inhibitors using multiscale milestoning and metadynamics simulations.

This study uses molecular dynamics simulations to explore the structural dynamics of mucins, revealing how O-glycosylation influences their bottlebrush-like conformation.

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

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 identifies a novel allosteric pocket on APOBEC3B using computational methods but finds that metal contamination in screening samples led to false positive inhibitor results.

The paper develops a pipeline using GAMer 2 to convert electron microscopy images into 3D meshes for reaction-diffusion simulations in realistic cellular geometries.