CHARMM at 45: Enhancements in accessibility, functionality, and speed
Since its inception nearly a half century ago, CHARMM has been playing a central role in
computational biochemistry and biophysics. Commensurate with the developments in …
computational biochemistry and biophysics. Commensurate with the developments in …
Filovirus entry: a novelty in the viral fusion world
CL Hunt, NJ Lennemann, W Maury - Viruses, 2012 - mdpi.com
Ebolavirus (EBOV) and Marburgvirus (MARV) that compose the filovirus family of negative
strand RNA viruses infect a broad range of mammalian cells. Recent studies indicate that …
strand RNA viruses infect a broad range of mammalian cells. Recent studies indicate that …
All-atom virus simulations
JA Hadden, JR Perilla - Current opinion in virology, 2018 - Elsevier
Highlights•Viral protein simulations are among the largest all-atom simulations ever
published.•All-atom simulations reveal the dynamics of viral proteins at chemical …
published.•All-atom simulations reveal the dynamics of viral proteins at chemical …
Host cell factors in filovirus entry: novel players, new insights
H Hofmann-Winkler, F Kaup, S Pöhlmann - Viruses, 2012 - mdpi.com
Filoviruses cause severe hemorrhagic fever in humans with high case-fatality rates. The
cellular factors exploited by filoviruses for their spread constitute potential targets for …
cellular factors exploited by filoviruses for their spread constitute potential targets for …
Dynamic heterogeneous dielectric generalized born (DHDGB): an implicit membrane model with a dynamically varying bilayer thickness
An extension to the heterogeneous dielectric generalized Born (HDGB) implicit membrane
formalism is presented to allow dynamic membrane deformations in response to membrane …
formalism is presented to allow dynamic membrane deformations in response to membrane …
Coupled folding-binding in a hydrophobic/polar protein model: impact of synergistic folding and disordered flanks
A Bhattacherjee, S Wallin - Biophysical journal, 2012 - cell.com
Coupled folding-binding is central to the function of many intrinsically disordered proteins,
yet not fully understood. With a continuous three-letter protein model, we explore the free …
yet not fully understood. With a continuous three-letter protein model, we explore the free …
Three conserved C-terminal residues of influenza fusion peptide alter its behavior at the membrane interface
R Worch, J Krupa, A Filipek, A Szymaniec… - Biochimica et Biophysica …, 2017 - Elsevier
The N-terminal fragment of the viral hemagglutinin HA2 subunit is termed a fusion peptide
(HAfp). The 23-amino acid peptide (HAfp1-23) contains three C-terminal W21-Y22-G23 …
(HAfp). The 23-amino acid peptide (HAfp1-23) contains three C-terminal W21-Y22-G23 …
NS2B/NS3 protease: allosteric effect of mutations associated with the pathogenicity of tick-borne encephalitis virus
UV Potapova, SI Feranchuk, VV Potapov… - Journal of …, 2012 - Taylor & Francis
The sequences of the protease domain of the tick-borne encephalitis (TBE) virus NS3
protein have two amino acid substitutions, 16 R→ K and 45 S→ F, in the highly pathogenic …
protein have two amino acid substitutions, 16 R→ K and 45 S→ F, in the highly pathogenic …
Understanding the Activated Form of a Class-I Fusion Protein: Modeling the Interaction of the Ebola Virus Glycoprotein 2 with a Lipid Bilayer
The fusion of the viral and target cell membranes is a key step in the life cycle of all
enveloped viruses. Here, a range of structural data is used to generate an evidence-based …
enveloped viruses. Here, a range of structural data is used to generate an evidence-based …
Heterogeneous dielectric generalized B orn model with a van der W aals term provides improved association energetics of membrane‐embedded transmembrane …
The heterogeneous dielectric generalized Born (HDGB) implicit membrane formalism is
extended by the addition of a van der Waals dispersion term to better describe the nonpolar …
extended by the addition of a van der Waals dispersion term to better describe the nonpolar …