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List of works by Rommie E Amaro

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

scientific article published on 06 April 2020

A Celebration of Women in Computational Chemistry

scientific article published on 01 May 2019

A Multiscale Coarse-grained Model of the SARS-CoV-2 Virion

scientific article published on 02 October 2020

An Integrated Markov State Model and Path Metadynamics Approach To Characterize Drug Binding Processes

scientific article published on 05 September 2019

Biography of Klaus Schulten.

scientific article published in April 2017

COVID19 - Computational Chemists Meet the Moment

scientific article published on 01 December 2020

Cation-Driven Lipopolysaccharide Morphological Changes Impact Heterogeneous Reactions of Nitric Acid with Sea Spray Aerosol Particles

scientific article

Conformational Switch Regulates the DNA Cytosine Deaminase Activity of Human APOBEC3B.

scientific article

D3R Grand Challenge 3: blind prediction of protein-ligand poses and affinity rankings

scientific article published on 10 January 2019

D3R grand challenge 4: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies

scientific article published on 23 January 2020

Determinants of Oligonucleotide Selectivity of APOBEC3B

scientific article published on 10 September 2018

Development of Dimethylisoxazole-Attached Imidazo[1,2-<i>a</i>]pyridines as Potent and Selective CBP/P300 Inhibitors

scientific article published on 19 April 2021

Dynamics and Molecular Mechanisms of p53 Transcriptional Activation

article

Editorial: Method and Data Sharing and Reproducibility of Scientific Results

scientific article published on 01 December 2020

Electrostatic Interactions as Mediators in the Allosteric Activation of Protein Kinase A RIα.

scientific article published on 21 February 2017

Faces of Contemporary CryoEM Information and Modeling

scientific article published on 01 May 2020

Frontiers in CryoEM Modeling

scientific article published on 13 June 2019

Gaussian Accelerated Molecular Dynamics in OpenMM

scientific article published in 2022

Gaussian-Accelerated Molecular Dynamics with the Weighted Ensemble Method: A Hybrid Method Improves Thermodynamic and Kinetic Sampling

scientific article published on 30 November 2021

Impact of the Journal of Chemical Information and Modeling Special Issue on Women in Computational Chemistry

scientific article published on 05 July 2020

Improving the Efficiency of Ligand-Binding Protein Design with Molecular Dynamics Simulations

scientific article published on 10 September 2019

Insights into the behavior of nonanoic acid and its conjugate base at the air/water interface through a combined experimental and theoretical approach

scientific article published on 15 June 2020

Molecular Simulations Reveal an Unresolved Conformation of the Type IA Protein Kinase A Regulatory Subunit and Suggest Its Role in the cAMP Regulatory Mechanism.

scientific article published on 29 June 2017

Neolymphostin A is a Covalent Phosphoinositide-3-kinase (PI3-K)/Mammalian Target of Rapamycin (mTOR) Dual Inhibitor that Employs an Unusual Electrophilic Vinylogous Ester

scientific article published on 28 November 2018

POVME 3.0: Software for Mapping Binding Pocket Flexibility.

scientific article

Protein Cofactors Are Essential for High-Affinity DNA Binding by the Nuclear Factor κB RelA Subunit.

scientific article

SARS-CoV-2 escape in vitro from a highly neutralizing COVID-19 convalescent plasma

scientific article published on 28 December 2020

SEEKR: Simulation Enabled Estimation of Kinetic Rates, A Computational Tool to Estimate Molecular Kinetics and Its Application to Trypsin-Benzamidine Binding.

scientific article published on 13 February 2017

Structural basis for ligand modulation of the CCR2 conformational landscape

scientific article published on 11 April 2019

Surfactant Charge Modulates Structure and Stability of Lipase-Embedded Monolayers at Marine-Relevant Aerosol Surfaces

scientific article published on 25 June 2019

The flexibility of ACE2 in the context of SARS-CoV-2 infection

scientific article published on 16 September 2020

Voyager – An Innovative Computational Resource for Artificial Intelligence &amp; Machine Learning Applications in Science and Engineering

scientific article published on 10 September 2023

Words Matter: On the Debate over Free Speech, Inclusivity, and Academic Excellence

scientific article published on 4 August 2022

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