2026· Methods in molecular biology· Vol 3061, pp.
115-132
· 0 citations
Medicine
TL;DR
In this study, molecular dynamics simulations and fragment molecular orbital calculations of hairpin DNA and three types of G-quadruplexes, which are involved in transcription and translation in the absence and presence of tetraethylene glycol(EG4) as crowding molecules, provide insight into how crowding molecules shape the intracellular environment surrounding nucleic acids.
Evaluating modern AMBER-based parametrizations across diverse structural motifs, including aptamers, duplexes, and quadruplex-duplex hybrids, provides critical insights for developing next-generation DNA force fields capable of accurately modeling non-native structures and enabling balanced sampling essential for predi...
G. Bekker, Y. Fukunishi, Junichi Higo et al.· Journal of Chemical Theory a...· 0 citations
A practical overview of classical atomistic MD methodologies commonly used in medicinal chemistry, including force-field-based simulations, enhanced sampling techniques, and free-energy calculation methods such as alchemical and end-point approaches are provided.
S. S. Çınaroğlu· Mini-Reviews in Medical Chem...· 1 citation
A generalized essential dynamics-refined ENM (edENM) is introduced for both DNA, RNA, and protein-nucleic acid complexes, parametrized against a diverse set of molecular dynamics simulations and validated using experimental ensembles from nuclear magnetic resonance, X-ray crystallography, and cryogenic electron microsc...
Domenico Scaramozzino, Marco Cannariato, Byung Ho Lee et al.· Nucleic Acids Research· 1 citation
Increasing knowledge of the wide range of biological functions of ribonucleic acids (RNAs) has made them a critical target in drug development. Accordingly, modifying their function by targeting them with small, drug-like molecules for the development of therapeutic agents is attractive. However, the rational design...
Jihyeon Lee, Alexander D. MacKerell· Journal of Chemical Theory a...· 0 citations
It is shown that short nucleic acids containing Gquadruplex (G4) structure can also catalyze protein folding and uncovers a previously underappreciated role for nucleic acid in proteostasis and offers a new strategy for studying nucleic acid structure-function relationship at residue level.
NACraft, a training-free and programmatic framework for all-atom nucleic-acid aptamer design based on backpropagation through structure-model feedback, is presented, demonstrating the effectiveness and versatility of NACraft and extending structure-model hallucination toward programmatic nucleic-acid aptamer design.
