[HTML][HTML] 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 …

Risk factors for recurrent intussusception in children: a retrospective cohort study

W Guo, Z Hu, Y Tan, M Sheng, J Wang - BMJ open, 2017 - bmjopen.bmj.com
Objective The aim of this study was to assess the frequency of clinical features and
pathological lead points in recurrent intussusception, with a special focus on the risk factors …

[PDF][PDF] A potassium-sensing niche in Arabidopsis roots orchestrates signaling and adaptation responses to maintain nutrient homeostasis

FL Wang, YL Tan, L Wallrad, XQ Du, A Eickelkamp… - Developmental cell, 2021 - cell.com
Organismal homeostasis of the essential ion K+ requires sensing of its availability, efficient
uptake, and defined distribution. Understanding plant K+ nutrition is essential to advance …

Receptor-like protein kinase BAK1 promotes K+ uptake by regulating H+-ATPase AHA2 under low potassium stress

ZF Wang, ZM Xie, YL Tan, JY Li, FL Wang… - Plant …, 2022 - academic.oup.com
Potassium (K+) is one of the essential macronutrients for plant growth and development.
However, the available K+ concentration in soil is relatively low. Plant roots can perceive low …

[PDF][PDF] rsRNASP: A residue-separation-based statistical potential for RNA 3D structure evaluation

YL Tan, X Wang, YZ Shi, W Zhang, ZJ Tan - Biophysical Journal, 2022 - cell.com
Abstract Knowledge-based statistical potentials have been shown to be rather effective in
protein 3-dimensional (3D) structure evaluation and prediction. Recently, several statistical …

cgRNASP: coarse-grained statistical potentials with residue separation for RNA structure evaluation

YL Tan, X Wang, S Yu, B Zhang… - NAR Genomics and …, 2023 - academic.oup.com
Abstract Knowledge-based statistical potentials are very important for RNA 3-dimensional
(3D) structure prediction and evaluation. In recent years, various coarse-grained (CG) and …

[HTML][HTML] Predicting 3D structure and stability of RNA pseudoknots in monovalent and divalent ion solutions

YZ Shi, L Jin, CJ Feng, YL Tan… - PLOS Computational …, 2018 - journals.plos.org
RNA pseudoknots are a kind of minimal RNA tertiary structural motifs, and their three-
dimensional (3D) structures and stability play essential roles in a variety of biological …

Predicting 3D structures and stabilities for complex RNA pseudoknots in ion solutions

X Wang, YL Tan, S Yu, YZ Shi, ZJ Tan - Biophysical Journal, 2023 - cell.com
RNA pseudoknots are a kind of important tertiary motif, and the structures and stabilities of
pseudoknots are generally critical to the biological functions of RNAs with the motifs. In this …

What is the best reference state for building statistical potentials in RNA 3D structure evaluation?

YL Tan, CJ Feng, L Jin, YZ Shi, W Zhang, ZJ Tan - RNA, 2019 - rnajournal.cshlp.org
Knowledge-based statistical potentials have been shown to be efficient in protein structure
evaluation/prediction, and the core difference between various statistical potentials is …

Structure folding of RNA kissing complexes in salt solutions: predicting 3D structure, stability, and folding pathway

L Jin, YL Tan, Y Wu, X Wang, YZ Shi, ZJ Tan - RNA, 2019 - rnajournal.cshlp.org
RNA kissing complexes are essential for genomic RNA dimerization and regulation of gene
expression, and their structures and stability are critical to their biological functions. In this …