Micronutrient status and breast cancer: a narrative review

A Forma, A Grunwald, P Zembala… - International Journal of …, 2024 - mdpi.com
Breast cancer is one of the most common cancers worldwide, at the same time being one of
the most prevalent causes of women's death. Many factors such as alcohol, weight …

Computational modeling of DNA 3D structures: From dynamics and mechanics to folding

ZC Mu, YL Tan, J Liu, BG Zhang, YZ Shi - Molecules, 2023 - mdpi.com
DNA carries the genetic information required for the synthesis of RNA and proteins and
plays an important role in many processes of biological development. Understanding the …

Binding of Phosphate Species to Ca2+ and Mg2+ in Aqueous Solution

B Koca Fındık, M Jafari, LF Song, Z Li… - Journal of Chemical …, 2024 - ACS Publications
Phosphate derivatives and their interaction with metal cations are involved in many
important biological phenomena, so an accurate characterization of the phosphate-metal …

Twisting DNA by salt

S Cruz-León, W Vanderlinden, P Müller… - Nucleic acids …, 2022 - academic.oup.com
The structure and properties of DNA depend on the environment, in particular the ion
atmosphere. Here, we investigate how DNA twist-one of the central properties of DNA …

Optimized magnesium force field parameters for biomolecular simulations with accurate solvation, ion-binding, and water-exchange properties in SPC/E, TIP3P-fb …

KK Grotz, N Schwierz - Journal of chemical theory and …, 2021 - ACS Publications
Magnesium is essential in many vital processes. To correctly describe Mg2+ in physiological
processes by molecular dynamics simulations, accurate force fields are fundamental …

Systematic analysis of biomolecular conformational ensembles with PENSA

M Vögele, NJ Thomson, ST Truong, J McAvity… - The Journal of …, 2025 - pubs.aip.org
Atomic-level simulations are widely used to study biomolecules and their dynamics. A
common goal in such studies is to compare simulations of a molecular system under several …

Frontiers and challenges of computing ncRNAs biogenesis, function and modulation

S Rinaldi, E Moroni, R Rozza… - Journal of Chemical …, 2024 - ACS Publications
Non-coding RNAs (ncRNAs), generated from nonprotein coding DNA sequences, constitute
98–99% of the human genome. Non-coding RNAs encompass diverse functional classes …

Establishing the catalytic and regulatory mechanism of RNA‐based machineries

J Borišek, J Aupič, A Magistrato - Wiley Interdisciplinary …, 2023 - Wiley Online Library
Ribonucleoprotein (RNP)‐machineries are comprised of intricate networks of long
noncoding RNAs and proteins that allow them to actively participate in transcription, RNA …

Consistent Picture of Phosphate–Divalent Cation Binding from Models with Implicit and Explicit Electronic Polarization

J Puyo-Fourtine, M Juillé, J Hénin… - The Journal of …, 2022 - ACS Publications
The binding of divalent cations to the ubiquitous phosphate group is essential for a number
of key biological processes, such as DNA compaction, RNA folding, or interactions of some …

[HTML][HTML] Magnesium force fields for OPC water with accurate solvation, ion-binding, and water-exchange properties: Successful transfer from SPC/E

KK Grotz, N Schwierz - The Journal of Chemical Physics, 2022 - pubs.aip.org
Magnesium plays a vital role in a large variety of biological processes. To model such
processes by molecular dynamics simulations, researchers rely on accurate force field …