G4-quadruplex-binding proteins: review and insights into selectivity
V Meier-Stephenson - Biophysical reviews, 2022 - Springer
There are over 700,000 putative G4-quadruplexes (G4Qs) in the human genome, found
largely in promoter regions, telomeres, and other regions of high regulation. Growing …
largely in promoter regions, telomeres, and other regions of high regulation. Growing …
Recent developments in empirical atomistic force fields for nucleic acids and applications to studies of folding and dynamics
AM Salsbury, JA Lemkul - Current opinion in structural biology, 2021 - Elsevier
Highlights•Nucleic acid force field development draws from theoretical and empirical data,
with increased reliance on experimental observables.•Nonpolarizable force fields are highly …
with increased reliance on experimental observables.•Nonpolarizable force fields are highly …
CHARMM‐GUI Drude prepper for molecular dynamics simulation using the classical Drude polarizable force field
Explicit treatment of electronic polarizability in empirical force fields (FFs) represents an
extension over a traditional additive or pairwise FF and provides a more realistic model of …
extension over a traditional additive or pairwise FF and provides a more realistic model of …
Differences in Conformational Sampling and Intrinsic Electric Fields Drive Ion Binding in Telomeric and TERRA G-Quadruplexes
The formation of G-quadruplexes (GQs) occurs in guanine-rich sequences of DNA and RNA,
producing highly stable and structurally diverse noncanonical nucleic acid structures. GQs …
producing highly stable and structurally diverse noncanonical nucleic acid structures. GQs …
Studying the dynamics of a complex G-Quadruplex system: Insights into the comparison of MD and NMR data
Molecular dynamics (MD) simulations are coming of age in the study of nucleic acids,
including specific tertiary structures such as G-quadruplexes. While being precious for …
including specific tertiary structures such as G-quadruplexes. While being precious for …
Polarizable Molecular Dynamics Simulations of Two c-kit Oncogene Promoter G-Quadruplexes: Effect of Primary and Secondary Structure on Loop and Ion Sampling
G-quadruplexes (GQs) are highly ordered nucleic acid structures that play fundamental roles
in regulating gene expression and maintaining genomic stability. GQs are topologically …
in regulating gene expression and maintaining genomic stability. GQs are topologically …
Benchmark force fields for the molecular dynamic simulation of G-quadruplexes
G-quadruplexes have drawn widespread attention for serving as a potential anti-cancer
target and their application in material science. Molecular dynamics (MD) simulation is the …
target and their application in material science. Molecular dynamics (MD) simulation is the …
Extension of the charmm classical drude polarizable force field to n-and o-linked glycopeptides and glycoproteins
AA Kognole, AH Aytenfisu… - The Journal of Physical …, 2022 - ACS Publications
Molecular dynamic simulations are an effective tool to study complex molecular systems and
are contingent upon the availability of an accurate and reliable molecular mechanics force …
are contingent upon the availability of an accurate and reliable molecular mechanics force …
Insights into G-quadruplex–hemin dynamics using atomistic simulations: implications for reactivity and folding
Guanine quadruplex nucleic acids (G4s) are involved in key biological processes such as
replication or transcription. Beyond their biological relevance, G4s find applications as …
replication or transcription. Beyond their biological relevance, G4s find applications as …
Balanced polarizable Drude force field parameters for molecular anions: phosphates, sulfates, sulfamates, and oxides
Polarizable force fields are emerging as a more accurate alternative to additive force fields
in terms of modeling and simulations of a variety of chemicals including biomolecules …
in terms of modeling and simulations of a variety of chemicals including biomolecules …