Ya-Lan Tan
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View article: gCoSRNA: Generalizable Coaxial-Stacking Prediction for RNA Junctions Using Secondary Structure
gCoSRNA: Generalizable Coaxial-Stacking Prediction for RNA Junctions Using Secondary Structure Open
Coaxial stacking between adjacent stems is a key tertiary interaction that defines the spatial organization of RNA junctions, which are core structural motifs in folded RNAs. Accurate prediction of coaxial stacking is critical for RNA 3D s…
View article: ABC2A: A Straightforward and Fast Method for the Accurate Backmapping of RNA Coarse-Grained Models to All-Atom Structures
ABC2A: A Straightforward and Fast Method for the Accurate Backmapping of RNA Coarse-Grained Models to All-Atom Structures Open
RNAs play crucial roles in various essential biological functions, including catalysis and gene regulation. Despite the widespread use of coarse-grained (CG) models/simulations to study RNA 3D structures and dynamics, their direct applicat…
View article: RNA 3D Structure Prediction: Progress and Perspective
RNA 3D Structure Prediction: Progress and Perspective Open
Ribonucleic acid (RNA) molecules play vital roles in numerous important biological functions such as catalysis and gene regulation. The functions of RNAs are strongly coupled to their structures or proper structure changes, and RNA structu…
View article: Computational Modeling of DNA 3D Structures: From Dynamics and Mechanics to Folding
Computational Modeling of DNA 3D Structures: From Dynamics and Mechanics to Folding Open
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 three-dimensional (3D) structures and dynamics of DNA is crucial …
View article: cgRNASP: coarse-grained statistical potentials with residue separation for RNA structure evaluation
cgRNASP: coarse-grained statistical potentials with residue separation for RNA structure evaluation Open
Knowledge-based statistical potentials are very important for RNA 3-dimensional (3D) structure prediction and evaluation. In recent years, various coarse-grained (CG) and all-atom models have been developed for predicting RNA 3D structures…
View article: Ab initio predictions for 3D structure and stability of single- and double-stranded DNAs in ion solutions
Ab initio predictions for 3D structure and stability of single- and double-stranded DNAs in ion solutions Open
The three-dimensional (3D) structure and stability of DNA are essential to understand/control their biological functions and aid the development of novel materials. In this work, we present a coarse-grained (CG) model for DNA based on the …
View article: <i>Ab initio</i> predictions for 3D structure and stability of single- and double-stranded DNAs in ion solutions
<i>Ab initio</i> predictions for 3D structure and stability of single- and double-stranded DNAs in ion solutions Open
The three-dimensional (3D) structure and stability of DNA are essential to understand/control their biological functions and aid the development of novel materials. In this work, we present a coarse-grained (CG) model for DNA based on the …
View article: FebRNA: an automated fragment-ensemble-based model for building RNA 3D structures
FebRNA: an automated fragment-ensemble-based model for building RNA 3D structures Open
Knowledge of RNA 3-dimensional (3D) structures is critical to understanding the important biological functions of RNAs. Although various structure prediction models have been developed, high accuracy of predicted RNA 3D structures is still…
View article: cgRNASP: coarse-grained statistical potentials with residue separation for RNA structure evaluation
cgRNASP: coarse-grained statistical potentials with residue separation for RNA structure evaluation Open
Knowledge-based statistical potentials are very important for RNA 3-dimensional (3D) structure prediction and evaluation. In recent years, various coarse-grained (CG) and all-atom models have been developed for predicting RNA 3D structures…
View article: RNAStat: An Integrated Tool for Statistical Analysis of RNA 3D Structures
RNAStat: An Integrated Tool for Statistical Analysis of RNA 3D Structures Open
The 3D architectures of RNAs are essential for understanding their cellular functions. While an accurate scoring function based on the statistics of known RNA structures is a key component for successful RNA structure prediction or evaluat…
View article: rsRNASP: A residue-separation-based statistical potential for RNA 3D structure evaluation
rsRNASP: A residue-separation-based statistical potential for RNA 3D structure evaluation Open
Knowledge-based statistical potentials have been shown to be rather effective in protein 3-dimensional (3D) structure evaluation and prediction. Recently, several statistical potentials have been developed for RNA 3D structure evaluation, …
View article: Salt-Dependent RNA Pseudoknot Stability: Effect of Spatial Confinement
Salt-Dependent RNA Pseudoknot Stability: Effect of Spatial Confinement Open
Macromolecules, such as RNAs, reside in crowded cell environments, which could strongly affect the folded structures and stability of RNAs. The emergence of RNA-driven phase separation in biology further stresses the potential functional r…
View article: Automatic Segmentation of Abdominal Subcutaneous Adipose Layer in Ultrasound Image Using CNN
Automatic Segmentation of Abdominal Subcutaneous Adipose Layer in Ultrasound Image Using CNN Open
Accurate measurement of the thickness of subcutaneous adipose tissue (SAT) can effectively estimate body composition. Ultrasound is an accurate technique for measuring the thickness of SAT layer. However, at different body sites, the SAT l…
View article: Structure folding of RNA kissing complexes in salt solutions: predicting 3D structure, stability, and folding pathway
Structure folding of RNA kissing complexes in salt solutions: predicting 3D structure, stability, and folding pathway Open
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 work, we used our previously developed coarse-graine…
View article: What is the best reference state for building statistical potentials in RNA 3D structure evaluation?
What is the best reference state for building statistical potentials in RNA 3D structure evaluation? Open
Knowledge-based statistical potentials have been shown to be efficient in protein structure evaluation/prediction, and the core difference between various statistical potentials is attributed to the choice of reference states. However, for…
Predicting 3D structure and stability of RNA pseudoknots in monovalent and divalent ion solutions Open
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 functions. Therefore, to predict 3D structures and stability of…