2024
Computational structural biology: Evolution of the field
Jodi A. Hadden-Perilla* and Juan R. Perilla*
* Corresponding authors
In press in Journal of Structural Biology.
Structural biology for researchers with low vision
Olivia R. Shaw, Cynthia Yurkovich, and Jodi A. Hadden-Perilla
Nature 2024, doi: 10.1038/d41586-024-00519-5.
Structural basis for nuclear import of Hepatitis B Virus (HBV) nucleocapsid core
Ruoyu Yang, Ying-Hui Ko, Fenglin Li, Ravi K. Lokareddy, Chun-Feng David Hou, Christine Kim, Shelby Klein, Santiago Antolinez, Carolina Perez-Segura, Martin F. Jarrold, Adam Zlotnick, Jodi A. Hadden-Perilla*, and Gino Cingolani*
* Corresponding authors
Science Advances 2024, 10(2):eadi7606.
AMBERff at scale: Multimillion-atom simulations with AMBER force fields in NAMD
Santiago Antolinez, Peter Eugene Jones, James C. Phillips, and Jodi A. Hadden-Perilla
Journal of Chemical Information and Modeling 2024, 64(2):543-554.
2023
Unsupervised Refinement of Protein Structures
Alexander J. Bryer, Juan S. Rey, Chaoyi Xu, Jodi A. Hadden-Perilla, and Juan R. Perilla
In Integrated Structural Biology (2023) 30(11), 327-347.
Royal Society of Chemistry Publishing, Cambridge, UK.
Structure of the Hepatitis B Virus capsid quasi-sixfold with a trapped C-terminal domain reveals capsid movements associated with domain exit
Christine Kim, Christopher J. Schlicksup, Carolina Perez-Segura, Jodi A. Hadden-Perilla, Joseph Che-Yen Wang, and Adam Zlotnick
Journal of Biological Chemistry 2023, 299(9):105104.
2022
Dynamic Regulation of Zn(II) Sequestration by Calgranulin C
Qian Wang, Deniz Kuci, Shibani Bhattacharya*, Jodi A. Hadden-Perilla*, and Rupal Gupta*
* Corresponding authors
Protein Science 2022, 31(9), e4403.
Multiscale Modeling of Hepatitis B Virus Capsid Assembly and its Dimorphism
Farzaneh Mohajerani, Botond Tyukodi, Christopher J. Schlicksup, Jodi A. Hadden-Perilla, Adam Zlotnick, and Michael F. Hagan
ACS Nano 2022, 16(9), 13845-13859.
Experimental Characterization of the Hepatitis B Virus Capsid Dynamics by Solid-State NMR
Alexander A. Malar, Morgane Callon, Albert A. Smith, Shishan Wang, Lauriane Lecoq, Carolina Perez-Segura, Jodi A. Hadden-Perilla, Anja Bockmann, and Beat H. Meier
Frontiers in Molecular Biosciences 2022, 8, 807577.
2021
A Subset of Fluorophores is Responsible for Radiation-Brightening in Viromimetic Particles
Arathi Anil Sushma, Bingqing Zhao, Irina Tsvetkova, Carolina Perez-Segura, Jodi A. Hadden-Perilla, James Reilly, and Bogdan Dragnea
Journal of Physical Chemistry B 2021, 125(37), 10494-10505.
Molecular dynamics of the viral life cycle: Progress and prospects
Peter Eugene Jones, Carolina Perez-Segura, Alexander J. Bryer, Juan R. Perilla, and Jodi A. Hadden-Perilla
Current Opinion in Virology 2021, 50, 128-138.
Integrative Structural Biology of HIV-1 Capsid Protein Assemblies: Combining Experiment and Computation
Juan R. Perilla, Jodi A. Hadden-Perilla, Angela M. Gronenborn, and Tatyana Polenova
Current Opinion in Virology 2021, 48, 57-64.
All-Atom MD Simulations of the HBV Capsid Complexed with AT130 Reveals Secondary and Tertiary Structural Changes and Mechanisms of Allostery
Carolina Perez-Segura, Boon Chong Goh, and Jodi A. Hadden-Perilla
Viruses 2021, 13(4), 564.
2020
Scalable Analysis of Authentic Viral Envelopes on FRONTERA
Fabio Gonzalez-Arias, Tyler Reddy, John E. Stone, Jodi A. Hadden-Perilla*, and Juan R. Perilla*
* Corresponding authors
Computing in Science and Engineering (2020) 22(6), 11-20.
Coronavirus through Delaware’s Computational Microscope
Carolina Perez-Segura, Nidhi Katyal, Fabio Gonzalez-Arias, Alexander J. Bryer, Juan R. Perilla, and Jodi A. Hadden-Perilla
Delaware Journal of Public Health (2020) 6(2A), 6-9.
TactViz: A VMD plugin for tactile visualization of protein structures
Olivia R. Shaw and Jodi A. Hadden-Perilla
Journal of Science Education for Students with Disabilities (2020) 23, 14.
The integrity of the intradimer interface of the hepatitis B virus capsid protein dimer regulates capsid self-assembly
Zhongchao Zhao, Joseph Che-Yen Wang, Carolina Perez-Segura, Jodi A. Hadden-Perilla*, and Adam Zlotnick*
* Corresponding authors
ACS Chemical Biology (2020) 15, 3124-3132.
2019
High-performance analysis of biomolecular containers to measure small-molecule transport, transbilayer lipid diffusion, and protein cavities
Alexander J. Bryer*, Jodi A. Hadden-Perilla*, John E. Stone, and Juan R. Perilla
* Co-first authors
Journal of Chemical Information and Modeling (2019) 59, 4328-4338.
2018
Assembly properties of hepatitis B virus core protein mutants correlate with their resistance to assembly-directed antivirals
Lu Ruan, Jodi A. Hadden*, and Adam Zlotnick*
* Corresponding authors
Journal of Virology (2018) 92, e01082-18.
All-atom simulations of viruses
Jodi A. Hadden* and Juan R. Perilla
* Corresponding author
Current Opinion in Virology (2018) 31, 82-91.
All-atom molecular dynamics of the HBV capsid reveals insights into biological function and cryo-EM resolution limits
Jodi A. Hadden*, Juan R. Perilla, Christopher John Schlicksup, Balasubramanian Venkatakrishnan, Adam Zlotnick, and Klaus Schulten
* Corresponding author
eLife (2018) 7, e32478.
Molecular dynamics simulations of protein-drug complexes: A computational protocol for investigating the interactions of small-molecule therapeutics with biological targets and biosensors
Jodi A. Hadden* and Juan R. Perilla
* Corresponding author
In Computational Drug Discovery and Design – Methods in Molecular Biology (2018) 1762, 245-270.
Humana Press, New York, NY.
2017 and earlier
New insights into influenza A specificity: An evolution of paradigms
Ye Ji, Yohanna J. B. White, Jodi A. Hadden, Oliver C. Grant, and Robert J. Woods
Current Opinion in Structural Biology (2017) 44, 219-231.
Angular measurements of the dynein ring reveal a stepping mechanism dependent on a flexible stalk
Lisa G. Lippert, Tali Dadosh, Jodi A. Hadden, Vishakha Karnawat, Benjamin T. Diroll, Christopher B. Murray, Erika L. F. Holzbaur, Klaus Schulten, Samara L. Reck-Peterson, and Yale E. Goldman
Proceedings of the National Academy of Sciences (2017) 114, E4564-E4573.
3D implementation of the symbol nomenclature for graphical representation of glycans
David F. Thieker, Jodi A. Hadden, Klaus Schulten, and Robert J. Woods
Glycobiology (2016) 26, 786-787.
Computational methodologies for real-space structural refinement of large macromolecular complexes
Boon Chong Goh*, Jodi A. Hadden*, Rafael C. Bernardi, Abhishek Singharoy, Ryan McGreevy, Till Rudack, C. Keith Cassidy, and Klaus Schulten
* Co-first authors
Annual Review of Biophysics (2016) 45, 253-278.
All-atom molecular dynamics of virus capsids as drug targets
Juan R. Perilla, Jodi A. Hadden, Boon Chong Goh, Christopher G. Mayne, and Klaus Schulten
Journal of Physical Chemistry Letters (2016) 7, 1836-1844.
Calculating binding free energies for protein-carbohydrate complexes
Jodi A. Hadden, Matthew B. Tessier, Elisa Fadda, and Robert J. Woods
In Glycoinformatics – Methods in Molecular Biology (2015) 1273, 431-465.
Humana Press, New York, NY.
Effect of microfibril twisting on theoretical powder diffraction patterns of cellulose I-beta
Jodi A. Hadden, Alfred D. French, and Robert J. Woods
Cellulose (2014) 21, 879-884.
Unraveling cellulose microfibrils: A twisted tale
Jodi A. Hadden, Alfred D. French, and Robert J. Woods
Biopolymers (2013) 99, 746-756.
