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Publications

  • Molecular Dynamics Simulations of Protein–Drug Complexes: A Computational Protocol for Investigating the Interactions of Small-Molecule Therapeutics with Biological Targets and Biosensors
    Jodi Hadden, Juan R. Perilla
    In: Computational Drug Discovery and Design , 2018 , Pages: 245-270
  • Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics
    Gongpu Zhao*, Juan R. Perilla*, Ernest Yufenyuy, Xin Meng, Bo Chen, Jiying Ning, Jinwoo Ahn, Angela M. Gronenborn, Klaus Schulten, Christopher Aiken, Peijun Zhang
    Nature , 2013 , 497 , Pages: 643-646
  • Quenching protein dynamics interferes with HIV capsid maturation
    Mingzhang Wang *, Caitlin M. Quinn*, Juan R. Perilla*, Huilan Zhang, Randall Shirra Jr., Guangjin Hou, In-Ja Byeon, Christopher L. Suiter, Sherimay Ablan, Emiko Urano, Theodore J. Nitz, Christopher Aiken, Eric O. Freed, Peijun Zhang, Klaus Schulten, Angela Gronenborn, Tatyana Polenova
    Nature Communications , 2017 , 8 , Pages: 1779
  • CryoEM structure of MxB reveals a novel oligomerization interface critical for HIV restriction
    Frances J. D. Alvarez, Shaoda He, Juan R. Perilla, Sooin Jang, Klaus Schulten, Alan N. Engelman, Sjors H. W. Scheres, Peijun Zhang
    Science Advances , 2017 , 9 , Pages: e1701264
  • CryoEM Structure Refinement by Integrating NMR Chemical Shifts with Molecular Dynamics Simulations
    Juan R. Perilla, Gongpu Zhao, Manman Lu, Jiying Ning, Guangjin Hou, In-Ja L. Byeon, Angela M. Gronenborn, Tatyana Polenova, Peijun Zhang
    Journal of Physical Chemistry B , 2017 , Pages: 10.1021/acs.jpcb.6b13105
  • Physical properties of the HIV-1 capsid from all-atom molecular dynamics simulations
    Juan R. Perilla, Klaus Schulten
    Nature Communications , 2017 , 8 , Pages: 15959
  • Length of encapsidated cargo impacts stability and structure of in vitro assembled Alphavirus core-like particles.
    Vamseedhar Rayaprolu, Alan Moore, Joseph Wang, Boon Chong Goh, Juan R. Perilla, Adam Zlotnick, Suchetana Mukhopadhyay
    Journal of Physics: Condensed Matter , 2017
  • GPU-accelerated molecular dynamics clustering analysis with openACC.
    John E. Stone, Juan R. Perilla, C. Keith Cassidy, Klaus Schulten
    In Parallel Programming with openACC, Elsevier, 2016; ISBN: 9780124103979 , 2016
  • HIV-1 Capsid Function is Regulated by Dynamics: Quantitative Atomic-Resolution Insights by Integrating Magic-Angle-Spinning NMR, QM/MM, and MD
    Huilan Zhang, Guangjin Hou, Manman Lu, Jinwoo Ahn, In-Ja L. Byeon, Christopher J. Langmead, Juan R. Perilla, Ivan Hung Peter, L. Gor’kov Zhehong, Gan William, W. Brey, David A. Case, Klaus Schulten, Angela M. Gronenborn, Tatyana Polenova
    Journal of the American Chemical Society , 2016 , 138 , Pages: 14066–14075
  • Contributions of charged residues in structurally dynamic capsid surface loops to Rous sarcoma virus assembly
    Katrina Heyrana, Boon Chong Goh, Juan R. Perilla, Tam-Linh Nguyen, Mathew England, Maria Bewley, Klaus Schulten, Rebecca Craven
    Journal of Virology , 2016 , Pages: 10.1128/JVI.00378-16
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Perilla Laboratory
Department of Chemistry & Biochemistry
University of Delaware
177 Brown Laboratory
Newark, DE 19716

HIGHLIGHTS

  • Lab researchers study the HIV-1 maturation process in the millisecond regime
  • Our group uses the most powerful super computers
  • CryoEM, a core technique in our lab wins the 2017 Chemistry Nobel prize
  • Group members reveal the structure of a human protein capable of stopping HIV-1.
  • Perilla performs the largest most accurate simulation ever published

UPCOMING EVENTS

  • Seminar: Owen Pornillos (University of Virginia)
  • Seminar: Rob Dick (Cornell University)

GALLERY

Gallery

Copyright 2017 – Perilla Lab – Department of Chemistry and Biochemistry, University of Delaware