AIMC Topic: Nucleic Acid Conformation

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Comparative Study of Single-stranded Oligonucleotides Secondary Structure Prediction Tools.

BMC bioinformatics
BACKGROUND: Single-stranded nucleic acids (ssNAs) have important biological roles and a high biotechnological potential linked to their ability to bind to numerous molecular targets. This depends on the different spatial conformations they can assume...

AliNA - a deep learning program for RNA secondary structure prediction.

Molecular informatics
Nowadays there are numerous discovered natural RNA variations participating in different cellular processes and artificial RNA, e. g., aptamers, riboswitches. One of the required tasks in the investigation of their functions and mechanism of influenc...

Predicting 3D RNA structure from the nucleotide sequence using Euclidean neural networks.

Biophysical journal
Fast and accurate 3D RNA structure prediction remains a major challenge in structural biology, mostly due to the size and flexibility of RNA molecules, as well as the lack of diverse experimentally determined structures of RNA molecules. Unlike DNA s...

Limit and screen sequences with high degree of secondary structures in DNA storage by deep learning method.

Computers in biology and medicine
BACKGROUND: In single-stranded DNAs/RNAs, secondary structures are very common especially in long sequences. It has been recognized that the high degree of secondary structures in DNA sequences could interfere with the correct writing and reading of ...

Gradient-mixing LEGO robots for purifying DNA origami nanostructures of multiple components by rate-zonal centrifugation.

PloS one
DNA origami purification is essential for many fields, including biophysics, molecular engineering, and therapeutics. The increasing interest in DNA origami has led to the development of rate-zonal centrifugation (RZC) as a scalable, high yield, and ...

Modular reconfiguration of DNA origami assemblies using tile displacement.

Science robotics
The power of natural evolution lies in the adaptability of biological organisms but is constrained by the time scale of genetics and reproduction. Engineeringartificial molecular machines should not only include adaptability as a core feature but als...

RNA independent fragment partition method based on deep learning for RNA secondary structure prediction.

Scientific reports
The non-coding RNA secondary structure largely determines its function. Hence, accuracy in structure acquisition is of great importance. Currently, this acquisition primarily relies on various computational methods. The prediction of the structures o...

DNA Origami Nanostructure Detection and Yield Estimation Using Deep Learning.

ACS synthetic biology
DNA origami is a milestone in DNA nanotechnology. It is robust and efficient in constructing arbitrary two- and three-dimensional nanostructures. The shape and size of origami structures vary. To characterize them, an atomic force microscope, a trans...

Research on RNA secondary structure predicting via bidirectional recurrent neural network.

BMC bioinformatics
BACKGROUND: RNA secondary structure prediction is an important research content in the field of biological information. Predicting RNA secondary structure with pseudoknots has been proved to be an NP-hard problem. Traditional machine learning methods...

Review of machine learning methods for RNA secondary structure prediction.

PLoS computational biology
Secondary structure plays an important role in determining the function of noncoding RNAs. Hence, identifying RNA secondary structures is of great value to research. Computational prediction is a mainstream approach for predicting RNA secondary struc...