A multi-modal coarse grained model of DNA flexibility mappable to the atomistic level
J Walther, PD Dans, A Balaceanu… - Nucleic acids …, 2020 - academic.oup.com
We present a new coarse grained method for the simulation of duplex DNA. The algorithm
uses a generalized multi-harmonic model that can represent any multi-normal distribution of …
uses a generalized multi-harmonic model that can represent any multi-normal distribution of …
The static and dynamic structural heterogeneities of B-DNA: extending Calladine–Dickerson rules
We present a multi-laboratory effort to describe the structural and dynamical properties of
duplex B-DNA under physiological conditions. By processing a large amount of atomistic …
duplex B-DNA under physiological conditions. By processing a large amount of atomistic …
The impact of sequence periodicity on DNA mechanics: investigating the origin of A-tract's curvature
T Gardasevic, A Noy - Nanoscale, 2024 - pubs.rsc.org
Periodic sequences in phase with DNA helical shape are prevalent in genomes due to their
capacity to modulate DNA elasticity on a global scale. However, how this occurs is not well …
capacity to modulate DNA elasticity on a global scale. However, how this occurs is not well …
Sequence-dependent properties of the RNA duplex
F Battistini, A Sala, A Hospital… - Journal of Chemical …, 2023 - ACS Publications
Sequence-dependent properties of the DNA duplex have been accurately described using
extensive molecular dynamics simulations. The RNA duplex meanwhile─ which is typically …
extensive molecular dynamics simulations. The RNA duplex meanwhile─ which is typically …
SerraNA: a program to determine nucleic acids elasticity from simulation data
V Velasco-Berrelleza, M Burman… - Physical Chemistry …, 2020 - pubs.rsc.org
The resistance of DNA to stretch, twist and bend is broadly well estimated by experiments
and is important for gene regulation and chromosome packing. However, their sequence …
and is important for gene regulation and chromosome packing. However, their sequence …
BioExcel Building Blocks Workflows (BioBB-Wfs), an integrated web-based platform for biomolecular simulations
Abstract We present BioExcel Building Blocks Workflows, a web-based graphical user
interface (GUI) offering access to a collection of transversal pre-configured biomolecular …
interface (GUI) offering access to a collection of transversal pre-configured biomolecular …
Sequence-specific dynamics of DNA response elements and their flanking sites regulate the recognition by AP-1 transcription factors
Abstract Activator proteins 1 (AP-1) comprise one of the largest families of eukaryotic basic
leucine zipper transcription factors. Despite advances in the characterization of AP-1 DNA …
leucine zipper transcription factors. Despite advances in the characterization of AP-1 DNA …
Thermodynamics of DNA hybridization from atomistic simulations
GH Zerze, FH Stillinger… - The Journal of Physical …, 2021 - ACS Publications
Studying DNA hybridization equilibrium at atomistic length scales, either via molecular
dynamics (MD) or through commonly used advanced sampling approaches, is notoriously …
dynamics (MD) or through commonly used advanced sampling approaches, is notoriously …
Effect of Microenvironment on the Geometrical Structure of d(A)5 d(T)5 and d(G)5 d(C)5 DNA Mini-Helixes and the Dickerson Dodecamer: A Density Functional …
We report a comprehensive quantum-chemical study on d (A) 5· d (T) 5 and d (G) 5· d (C) 5
DNA mini-helixes and the Dickerson dodecamer d [CGCGAATTCGCG]. The research was …
DNA mini-helixes and the Dickerson dodecamer d [CGCGAATTCGCG]. The research was …