Physical properties of the HIV-1 capsid from all-atom molecular dynamics simulations

CryoEM Structure Refinement by Integrating NMR Chemical Shifts with Molecular Dynamics Simulations

(2017) Juan R. Perilla et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Computational virology: From the inside out

(2016) Tyler Reddy et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

All-Atom Molecular Dynamics of Virus Capsids as Drug Targets

(2016) Juan R. Perilla et al.   Journal of Physical Chemistry Letters

Contributions of Charged Residues in Structurally Dynamic Capsid Surface Loops to Rous Sarcoma Virus Assembly

(2016) Katrina J. Heyrana et al.   JOURNAL OF VIROLOGY

HIV-1 uses dynamic capsid pores to import nucleotides and fuel encapsidated DNA synthesis

(2016) David A. Jacques et al.   NATURE

Molecular Architecture of the Retroviral Capsid

(2016) Juan R. Perilla et al.   TRENDS IN BIOCHEMICAL SCIENCES

Coarse-grained simulation reveals key features of HIV-1 capsid self-assembly

(2016) John M. A. Grime et al.   Nature Communications

Cyclophilin A stabilizes the HIV-1 capsid through a novel non-canonical binding site

(2016) Chuang Liu et al.   Nature Communications

Physical Principles in the Self-Assembly of a Simple Spherical Virus

(2015) Rees F. Garmann et al.   ACCOUNTS OF CHEMICAL RESEARCH

Mechanism of polymorphism and curvature of HIV capsid assemblies probed by 3D simulations with a novel coarse grain model

(2015) Xin Qiao et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

Molecular dynamics simulations of large macromolecular complexes

(2015) Juan R Perilla et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

HIV-1 assembly, release and maturation

(2015) Eric O. Freed   NATURE REVIEWS MICROBIOLOGY

HIV-1 capsid: the multifaceted key player in HIV-1 infection

(2015) Edward M. Campbell et al.   NATURE REVIEWS MICROBIOLOGY

Dynamic allostery governs cyclophilin A–HIV capsid interplay

(2015) Manman Lu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

X-ray crystal structures of native HIV-1 capsid protein reveal conformational variability

(2015) A. T. Gres et al.   SCIENCE

Physics of Viral Shells

(2015) Robijn F. Bruinsma et al.   Annual Review of Condensed Matter Physics

All-atom molecular dynamics calculation study of entire poliovirus empty capsids in solution

(2014) Y. Andoh et al.   JOURNAL OF CHEMICAL PHYSICS

Determining Structural and Mechanical Properties from Molecular Dynamics Simulations of Lipid Vesicles

(2014) Anthony R. Braun et al.   Journal of Chemical Theory and Computation

A model for cofactor use during HIV-1 reverse transcription and nuclear entry

(2014) Laura Hilditch et al.   Current Opinion in Virology

The Interferon-Inducible MxB Protein Inhibits HIV-1 Infection

(2013) Zhenlong Liu et al.   Cell Host & Microbe

HIV-1 evades innate immune recognition through specific cofactor recruitment

(2013) Jane Rasaiyaah et al.   NATURE

Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics

(2013) Gongpu Zhao et al.   NATURE

Human MX2 is an interferon-induced post-entry inhibitor of HIV-1 infection

(2013) Caroline Goujon et al.   NATURE

MX2 is an interferon-induced inhibitor of HIV-1 infection

(2013) Melissa Kane et al.   NATURE

Extreme Genetic Fragility of the HIV-1 Capsid

(2013) Suzannah J. Rihn et al.   PLoS Pathogens

Exploring the Symmetry and Mechanism of Virus Capsid Maturation Via an Ensemble of Pathways

(2012) Eric R. May et al.   BIOPHYSICAL JOURNAL

Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ1 and χ2 Dihedral Angles

(2012) Robert B. Best et al.   Journal of Chemical Theory and Computation

The Host Proteins Transportin SR2/TNPO3 and Cyclophilin A Exert Opposing Effects on HIV-1 Uncoating

(2012) V. B. Shah et al.   JOURNAL OF VIROLOGY

CPSF6 Defines a Conserved Capsid Interface that Modulates HIV-1 Replication

(2012) Amanda J. Price et al.   PLoS Pathogens

Atomic-level modelling of the HIV capsid

(2011) Owen Pornillos et al.   NATURE

Salt-Dependent DNA-DNA Spacings in Intact BacteriophageλReflect Relative Importance of DNA Self-Repulsion and Bending Energies

(2011) Xiangyun Qiu et al.   PHYSICAL REVIEW LETTERS

HIV-1 Capsid-Cyclophilin Interactions Determine Nuclear Import Pathway, Integration Targeting and Replication Efficiency

(2011) Torsten Schaller et al.   PLoS Pathogens

Global Dynamics of Proteins: Bridging Between Structure and Function

(2010) Ivet Bahar et al.   Annual Review of Biophysics

Computing ensembles of transitions from stable states: Dynamic importance sampling

(2010) Juan R. Perilla et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Physical virology

(2010) W. H. Roos et al.   Nature Physics

Evidence for a third sodium-binding site in glutamate transporters suggests an ion/substrate coupling model

(2010) H. P. Larsson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural Convergence between Cryo-EM and NMR Reveals Intersubunit Interactions Critical for HIV-1 Capsid Function

(2009) In-Ja L. Byeon et al.   CELL

X-Ray Structures of the Hexameric Building Block of the HIV Capsid

(2009) Owen Pornillos et al.   CELL

SPRINT: A new parallel framework for R

(2008) Jon Hill et al.   BMC BIOINFORMATICS

The Mechanism of a Neurotransmitter:Sodium Symporter—Inward Release of Na+ and Substrate Is Triggered by Substrate in a Second Binding Site

(2008) Lei Shi et al.   MOLECULAR CELL

Low Frequency Mechanical Modes of Viral Capsids: An Atomistic Approach

(2008) Eric C. Dykeman et al.   PHYSICAL REVIEW LETTERS