Rommie E. Amaro

A Unified 3D Generative Model for Synthesizable Structure-Based Drug Design

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

seekrflow: Towards end-to-end automated simulation pipeline with machine-learned force fields for accelerated drug-target kinetic and thermodynamic predictions

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

D614G reshapes allosteric networks and opening mechanisms of SARS-CoV-2 spikes

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.

Condensate-Like Organization in Respiratory Aerosols Modulates the Dynamics of an Airborne Virus

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

Structural Dynamics and Allosteric Communication of a SARS-Like Bat Coronavirus Spike Glycoprotein

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.

Towards In Situ Dynamics of DNA-bound Full-Length p53 Tetramer

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.

pH-induced structural changes in SARS-CoV-2 spike variants

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.

An unconventional HxD motif orchestrates coatomer-dependent coronavirus morphogenesis

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

Markovian State Models uncover Casein Kinase 1 dynamics that govern circadian period

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.

Conformational dynamics and activation of membrane-associated human Group IVA cytosolic phospholipase A2 (cPLA2)

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

Cryo-EM visualizes multiple steps of dynein activation pathway

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

N-Glycans Modulate HIV-1 Env Conformational Plasticity

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.

Regulatory interactions between APOBEC3B N- and C-terminal domains

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

SARS CoV-2 spike adopts distinct conformational ensembles in situ

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.

An in vitro platform for the enzymatic characterization of the rhomboid protease RHBDL4

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

Distinct pathway for evolution of enhanced receptor binding and cell entry in SARS-like bat coronaviruses

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

Prediction of Threonine-Tyrosine Kinase Receptor-LigandUnbinding Kinetics with Multiscale Milestoning andMetadynamics

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

Breaking Down the Bottlebrush: Atomically-Detailed Structural Dynamics of Mucins

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

Computational Discovery of an Allosteric Pocket on APOBEC3B and the Impact of Metal Contamination on Inhibitor Validation

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.

3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries

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