- Home
- Publications
- Publication Search
- Publication Details
Title
Molecular dynamics of the viral life cycle: progress and prospects
Authors
Keywords
-
Journal
Current Opinion in Virology
Volume 50, Issue -, Pages 128-138
Publisher
Elsevier BV
Online
2021-08-29
DOI
10.1016/j.coviro.2021.08.003
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- Wrapping Up Viruses at Multiscale Resolution: Optimizing PACKMOL and SIRAH Execution for Simulating the Zika Virus
- (2021) Martín Soñora et al. Journal of Chemical Information and Modeling
- Capsid opening enables genome release of iflaviruses
- (2021) Karel Škubník et al. Science Advances
- AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics
- (2021) Lorenzo Casalino et al. INTERNATIONAL JOURNAL OF HIGH PERFORMANCE COMPUTING APPLICATIONS
- Viral packaging ATPases utilize a glutamate switch to couple ATPase activity and DNA translocation
- (2021) Joshua Pajak et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- All-Atom MD Simulations of the HBV Capsid Complexed with AT130 Reveal Secondary and Tertiary Structural Changes and Mechanisms of Allostery
- (2021) Carolina Pérez-Segura et al. Viruses-Basel
- The SARS-CoV-2 Spike variant D614G favors an open conformational state
- (2021) Rachael A. Mansbach et al. Science Advances
- Atomistic dynamics of a viral infection process: Release of membrane lytic peptides from a non-enveloped virus
- (2021) Asis K. Jana et al. Science Advances
- Curvature of the Retroviral Capsid Assembly Is Modulated by a Molecular Switch
- (2021) Tyrone Thames et al. Journal of Physical Chemistry Letters
- Atomistic basis of force generation, translocation, and coordination in a viral genome packaging motor
- (2021) Joshua Pajak et al. NUCLEIC ACIDS RESEARCH
- How a Virus Circumvents Energy Barriers to Form Symmetric Shells
- (2020) Sanaz Panahandeh et al. ACS Nano
- On virus growth and form
- (2020) Roya Zandi et al. PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS
- Conformational changes in the Ebola virus membrane fusion machine induced by pH, Ca2+, and receptor binding
- (2020) Dibyendu Kumar Das et al. PLOS BIOLOGY
- Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly
- (2020) Robert A. Dick et al. PLoS Pathogens
- Mesoscale All-Atom Influenza Virus Simulations Suggest New Substrate Binding Mechanism
- (2020) Jacob D. Durrant et al. ACS Central Science
- The integrity of the intradimer interface of the Hepatitis B Virus capsid protein dimer regulates capsid self-assembly
- (2020) Zhongchao Zhao et al. ACS Chemical Biology
- Quantitative Study of the Chiral Organization of the Phage Genome Induced by the Packaging Motor
- (2020) Brian Cruz et al. BIOPHYSICAL JOURNAL
- Multiscale modelling and simulation of viruses
- (2020) Jan K Marzinek et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
- Exploring the Reaction Mechanism of HIV Reverse Transcriptase with a Nucleotide Substrate
- (2020) Hao Wang et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Influenza hemagglutinin drives viral entry via two sequential intramembrane mechanisms
- (2020) Anna Pabis et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Markov State Model of Lassa Virus Nucleoprotein Reveals Large Structural Changes during the Trimer to Monomer Transition
- (2020) Jason G. Pattis et al. STRUCTURE
- Acquired Functional Capsid Structures in Metazoan Totivirus-like dsRNA Virus
- (2020) Kenta Okamoto et al. STRUCTURE
- Discovery of New Hydroxyethylamine Analogs against 3CLpro Protein Target of SARS-CoV-2: Molecular Docking, Molecular Dynamics Simulation, and Structure–Activity Relationship Studies
- (2020) Sumit Kumar et al. Journal of Chemical Information and Modeling
- SARS-CoV-2 Main Protease: A Molecular Dynamics Study
- (2020) Dimas Suárez et al. Journal of Chemical Information and Modeling
- Electrostatics Plays a Crucial Role in HIV-1 Protease Substrate Binding, Drugs Fail to Take Advantage
- (2020) Mohd Ahsan et al. BIOCHEMISTRY
- Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 Mpro
- (2020) Olivier Sheik Amamuddy et al. Journal of Chemical Information and Modeling
- Conformational transition of SARS-CoV-2 spike glycoprotein between its closed and open states
- (2020) Mert Gur et al. JOURNAL OF CHEMICAL PHYSICS
- Molecular determinants of Ebola nucleocapsid stability from molecular dynamics simulations
- (2020) Chaoyi Xu et al. JOURNAL OF CHEMICAL PHYSICS
- Acidic pH-induced conformational changes in chikungunya virus fusion protein, E1 – a spring-twisted region in the domain I-III linker acts as a hinge point for swivelling motion of domains
- (2020) Bibekananda Sahoo et al. JOURNAL OF VIROLOGY
- Analysis of the SARS-CoV-2 spike protein glycan shield reveals implications for immune recognition
- (2020) Oliver C. Grant et al. Scientific Reports
- Beyond Shielding: The Roles of Glycans in the SARS-CoV-2 Spike Protein
- (2020) Lorenzo Casalino et al. ACS Central Science
- An Alternative HIV-1 Non-Nucleoside Reverse Transcriptase Inhibition Mechanism: Targeting the p51 Subunit
- (2020) Kwok-Fong Chan et al. MOLECULES
- Permeability of the HIV-1 capsid to metabolites modulates viral DNA synthesis
- (2020) Chaoyi Xu et al. PLOS BIOLOGY
- The flexibility of ACE2 in the context of SARS-CoV-2 infection
- (2020) Emilia P. Barros et al. BIOPHYSICAL JOURNAL
- A multiscale coarse-grained model of the SARS-CoV-2 virion
- (2020) Alvin Yu et al. BIOPHYSICAL JOURNAL
- Enterovirus particles expel capsid pentamers to enable genome release
- (2019) David Buchta et al. Nature Communications
- FEZ1 Is Recruited to a Conserved Cofactor Site on Capsid to Promote HIV-1 Trafficking
- (2019) Pei-Tzu Huang et al. Cell Reports
- Gaussian curvature and the budding kinetics of enveloped viruses
- (2019) Sanjay Dharmavaram et al. PLoS Computational Biology
- High-Performance Analysis of Biomolecular Containers to Measure Small-Molecule Transport, Transbilayer Lipid Diffusion, and Protein Cavities
- (2019) Alexander J. Bryer et al. Journal of Chemical Information and Modeling
- Heteroaryldihydropyrimidines Alter Capsid Assembly By Adjusting the Binding Affinity and Pattern of the Hepatitis B Virus Core Protein
- (2019) Huihui Liu et al. Journal of Chemical Information and Modeling
- Energetics of Flap Opening in HIV-1 Protease: String Method Calculations
- (2019) Jasmine M. Gardner et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Hemagglutinin-Mediated Membrane Fusion: A Biophysical Perspective
- (2018) Sander Boonstra et al. Annual Review of Biophysics
- Ligand Binding Pathways and Conformational Transitions of the HIV Protease
- (2018) Yinglong Miao et al. BIOCHEMISTRY
- Why Enveloped Viruses Need Cores—The Contribution of a Nucleocapsid Core to Viral Budding
- (2018) Guillermo R. Lázaro et al. BIOPHYSICAL JOURNAL
- Identification of Factors Promoting HBV Capsid Self-Assembly by Assembly-Promoting Antivirals
- (2018) Soumya Lipsa Rath et al. Journal of Chemical Information and Modeling
- Critical Role of the Human T-Cell Leukemia Virus Type 1 Capsid N-Terminal Domain for Gag-Gag Interactions and Virus Particle Assembly
- (2018) Jessica L. Martin et al. JOURNAL OF VIROLOGY
- Atomistic simulations indicate the functional loop-to-coiled-coil transition in influenza hemagglutinin is not downhill
- (2018) Xingcheng Lin et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Multiscale modelization in a small virus: Mechanism of proton channeling and its role in triggering capsid disassembly
- (2018) Juan Francisco Viso et al. PLoS Computational Biology
- Allostery in the dengue virus NS3 helicase: Insights into the NTPase cycle from molecular simulations
- (2018) Russell B. Davidson et al. PLoS Computational Biology
- All-atom molecular dynamics of the HBV capsid reveals insights into biological function and cryo-EM resolution limits
- (2018) Jodi A Hadden et al. eLife
- Glycan binding and specificity of viral influenza neuraminidases by classical molecular dynamics and replica exchange molecular dynamics simulations
- (2018) Jiraphorn Phanich et al. JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
- Assembly Properties of Hepatitis B Virus Core Protein Mutants Correlate with Their Resistance to Assembly-Directed Antivirals
- (2018) Lu Ruan et al. JOURNAL OF VIROLOGY
- Inositol phosphates are assembly co-factors for HIV-1
- (2018) Robert A. Dick et al. NATURE
- Entropic forces drive clustering and spatial localization of influenza A M2 during viral budding
- (2018) Jesper J. Madsen et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- All-atom virus simulations
- (2018) Jodi A Hadden et al. Current Opinion in Virology
- Unbinding Dynamics of Non-Nucleoside Inhibitors from HIV-1 Reverse Transcriptase
- (2018) Leela S. Dodda et al. JOURNAL OF PHYSICAL CHEMISTRY B
- A Computational Assay that Explores the Hemagglutinin/Neuraminidase Functional Balance Reveals the Neuraminidase Secondary Site as a Novel Anti-Influenza Target
- (2018) Rommie E. Amaro et al. ACS Central Science
- Pyrophosphate Release in the Protein HIV Reverse Transcriptase
- (2017) Murat Atis et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Immature HIV-1 lattice assembly dynamics are regulated by scaffolding from nucleic acid and the plasma membrane
- (2017) Alexander J. Pak et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Physical properties of the HIV-1 capsid from all-atom molecular dynamics simulations
- (2017) Juan R. Perilla et al. Nature Communications
- Quenching protein dynamics interferes with HIV capsid maturation
- (2017) Mingzhang Wang et al. Nature Communications
- Computational virology: From the inside out
- (2016) Tyler Reddy et al. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
- Influence of RNA Binding on the Structure and Dynamics of the Lassa Virus Nucleoprotein
- (2016) Jason G. Pattis et al. BIOPHYSICAL JOURNAL
- Homology modeling and molecular dynamics provide structural insights into tospovirus nucleoprotein
- (2016) Rayane Nunes Lima et al. BMC BIOINFORMATICS
- Molecular Dynamics Simulations to Determine the Structure and Dynamics of Hepatitis B Virus Capsid Bound to a Novel Anti-viral Drug
- (2016) Go Watanabe et al. CHEMICAL & PHARMACEUTICAL BULLETIN
- Microsecond Molecular Dynamics Simulations of Influenza Neuraminidase Suggest a Mechanism for the Increased Virulence of Stalk-Deletion Mutants
- (2016) Jacob D. Durrant et al. JOURNAL OF PHYSICAL CHEMISTRY B
- 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
- Mechanism of membrane fusion induced by vesicular stomatitis virus G protein
- (2016) Irene S. Kim et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- The Role of the Membrane in the Structure and Biophysical Robustness of the Dengue Virion Envelope
- (2016) Tyler Reddy et al. STRUCTURE
- Recent advances in coarse-grained modeling of virus assembly
- (2016) Michael F Hagan et al. Current Opinion in Virology
- Enhanced sampling techniques in molecular dynamics simulations of biological systems
- (2015) Rafael C. Bernardi et al. BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
- The Robust Assembly of Small Symmetric Nanoshells
- (2015) Jef Wagner et al. BIOPHYSICAL JOURNAL
- Self-Assembly Molecular Dynamics Simulations Shed Light into the Interaction of the Influenza Fusion Peptide with a Membrane Bilayer
- (2015) Bruno L. Victor et al. Journal of Chemical Information and Modeling
- The Role of Packaging Sites in Efficient and Specific Virus Assembly
- (2015) Jason D. Perlmutter et al. JOURNAL OF MOLECULAR BIOLOGY
- Enzyme Selectivity of HIV Reverse Transcriptase: Conformations, Ligands, and Free Energy Partition
- (2015) Serdal Kirmizialtin et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Nothing to Sneeze At: A Dynamic and Integrative Computational Model of an Influenza A Virion
- (2015) Tyler Reddy et al. STRUCTURE
- Insight into the binding modes of Lassa nucleoprotein complexed with ssRNA by molecular dynamic simulations and free energy calculations
- (2014) Ying Zhang et al. JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
- Exploring the early stages of the pH-induced conformational change of influenza hemagglutinin
- (2014) Yu Zhou et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- Studies on the binding modes of Lassa nucleoprotein complexed with m7GpppG and dTTP by molecular dynamic simulations and free energy calculations
- (2012) Liang Li et al. JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
- Screening for the Location of RNA using the Chloride Ion Distribution in Simulations of Virus Capsids
- (2012) Daniel S. D. Larsson et al. Journal of Chemical Theory and Computation
- Unclosed HIV-1 Capsids Suggest a Curled Sheet Model of Assembly
- (2012) Zhiheng Yu et al. JOURNAL OF MOLECULAR BIOLOGY
- A model for the structure of satellite tobacco mosaic virus
- (2012) Yingying Zeng et al. JOURNAL OF STRUCTURAL BIOLOGY
- Equilibrium Sampling in Biomolecular Simulations
- (2011) Daniel M. Zuckerman Annual Review of Biophysics
- Multiscale Computer Simulation of the Immature HIV-1 Virion
- (2010) Gary S. Ayton et al. BIOPHYSICAL JOURNAL
- Structural and electrostatic characterization of Pariacoto virus: Implications for viral assembly
- (2009) Batsal Devkota et al. BIOPOLYMERS
Find Funding. Review Successful Grants.
Explore over 25,000 new funding opportunities and over 6,000,000 successful grants.
ExploreFind the ideal target journal for your manuscript
Explore over 38,000 international journals covering a vast array of academic fields.
Search