R Qian, J Xue, Y Xu, J Huang - Journal of Chemical Information …, 2024 - ACS Publications
Computational methods constitute efficient strategies for screening and optimizing potential drug molecules. A critical factor in this process is the binding affinity between candidate …
Z Jing, R Qi, M Thibonnier, P Ren - Journal of chemical theory and …, 2019 - ACS Publications
MicroRNAs (miRNAs) are attractive drug candidates for many diseases as they can modulate the expression of gene networks. Recently, we discovered that DNAs targeting …
Y Li, K Nam - Journal of chemical theory and computation, 2020 - ACS Publications
In alchemical free energy (FE) simulations, annihilation and creation of atoms are generally achieved with the soft-core potential that shifts the interparticle separations. While this soft …
P Mangla, B Olety, VK Sharma - Current Organic Chemistry, 2021 - benthamdirect.com
Bridged Nucleic Acids (BNA) or Locked Nucleic Acids (LNA) belong to a class of nucleic acid modification that is obtained by connecting the 2'-O and 4'-C of ribose sugar using a …
SR Manjari, NK Banavali - Journal of Chemical Information and …, 2018 - ACS Publications
A strategy named “restrained geometries and topology switching”(RGATS) is presented to obtain detailed trajectories for complex biochemical reactions using molecular mechanics …
The protonation states for nucleic acid bases are difficult to assess experimentally. In the context of DNA triplex, the protonation state of cytidine in the third strand is particularly …
Metal ions and nucleic acids are essential for a variety of biological functions. Metal ions play roles in enzyme catalysis, signal transduction and muscle contraction, and the …
L Nilsson, A Villa - Oligonucleotide-Based Therapies: Methods and …, 2019 - Springer
Molecular dynamics simulations with a state-of-the-art force field provide an atomistic detailed description of the structural and thermodynamic features of biomolecules. Effects of …