Publications

• Z. Ghaemi (corresponding author) and M. Gruebele, A Spatial Whole-Cell Model for HBV Viral Infection and Drug Interactions, bioRxiv, Submitted, 2022

• G. Gopan*, Z. Ghaemi*, C. Davis, and M. Gruebele
  Spliceosomal SL1 RNA binding to U1-70K: the role of the extended RRM, Nucleic Acids Res, In press, 2022.

• Z. Ghaemi, M. Gruebele and E. Tajkhorshid

Molecular mechanisms of virus capsid disassembly, Proc Nat Acad Sci,118, e2102530118, 2021

Featured in UIUC News, Phys.org, EurekAlert, Technology Networks, SCIEMAG, Florida News Times

• Z. Ghaemi, J. Peterson, M. Gruebele and Z. Luthey-Schulten

An in-silico mammalian whole-cell model reveals the influence of spatial organization on RNA splicing efficiency, PLoS Comput Biol, 16, e1007717, 2020

Featured in UIUC News, Phys.org, EurekAlert

• J. Lai*, Z. Ghaemi* and Z. Luthey-Schulten

The Conformational Change in Elongation Factor Tu Involves Separation of Its Domains, Biochemistry, 56, 5972, 2017

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• Z. Ghaemi, I. Guzman, Z. Luthey-Schulten and M. Gruebele,

Role of Electrostatics in Protein–RNA Binding: The Global vs the Local Energy Landscape, J Phys Chem B, 121, 8437-8446, 2017

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• Z. Ghaemi, I. Guzman, J. Baek, M. Gruebele and Z. Luthey-Schulten,

Estimation of relative protein–RNA binding strengths from fluctuations in the bound state, J Chem Theory Comp, 12, 4593–4599, 2016

• Z. Ghaemi, D. Alberga, P. Carloni, A. Laio and G. Lattanzi,

Predicting the permeability coefficient of pharmacologically relevant molecules using atomistic simulations, J Chem Theory Comp, 12, 4093–4099, 2016

• I. Guzman*, Z. Ghaemi*, A. Baranger, Z. Luthey-Schulten and M. Gruebele,

Conformational dynamics of the spliceosomal U1A protein, J Phys Chem B, 119, 3651-3661, 2015

• H. Zhao, A. Palencia, E. Seiradake, Z. Ghaemi, S. Cusack, Z. Luthey-Schulten and S. Martinis, Analysis of the Resistance Mechanism of a Benzoxaborole Inhibitor Reveals Insight into the Leucyl-tRNA Synthetase Editing Mechanism, ACS Chem Biol,10, 2277–2285, 2015

• Z. Ghaemi, M. Minozzi, P. Carloni and A. Laio,

A novel approach to the investigation of passive molecular permeation through lipid bilayers from atomistic simulation, J Phys Chem B, 116, 8714-8721, 2012

Featured on cover

• P. Lupieri*, C. Ha Huang Nguyen*, Z. Ghaemi*, A. Giorgetti and P. Carloni,

Computational molecular biology approaches to ligand-target interactions, HFSP J. 3, 228-239, 2009 (*equally contributed)