Related papers: Towards de novo RNA 3D structure prediction
Many recent exciting discoveries have revealed the versatility of RNAs and their importance in a variety of cellular functions which are strongly coupled to RNA structures. To understand the functions of RNAs, some structure prediction…
Structured RNA plays many functionally relevant roles in molecular life. Structural information, while required to understand the functional cycles in detail, is challenging to gather. Computational methods promise to complement…
RNA molecules are essential cellular machines performing a wide variety of functions for which a specific three-dimensional structure is required. Over the last several years, experimental determination of RNA structures through X-ray…
Predicting the 3D structure of a macromolecule, such as a protein or an RNA molecule, is ranked top among the most difficult and attractive problems in bioinformatics and computational biology. Its importance comes from the relationship…
The Human Genome Project has led to an exponential increase in data related to the sequence, structure, and function of biomolecules. Bioinformatics is an interdisciplinary research field that primarily uses computational methods to analyze…
RNAs play crucial and versatile roles in biological processes. Computational prediction approaches can help to understand RNA structures and their stabilizing factors, thus providing information on their functions, and facilitating the…
Understanding the connection between complex structural features of RNA and biological function is a fundamental challenge in evolutionary studies and in RNA design. However, building datasets of RNA 3D structures and making appropriate…
Accurate prediction of RNA three-dimensional (3D) structure remains an unsolved challenge. Determining RNA 3D structures is crucial for understanding their functions and informing RNA-targeting drug development and synthetic biology design.…
The relationship between RNA structure and function has recently attracted interest within the deep learning community, a trend expected to intensify as nucleic acid structure models advance. Despite this momentum, the lack of standardized,…
The structure of an RNA molecule plays a significant role in its biological function. Predicting structure given a one dimensional sequence of RNA nucleotide bases is a difficult and important problem. Many computer programs (known as in…
Structural prediction has long been considered critical in RNA research, especially following the success of AlphaFold2 in protein studies, which has drawn significant attention to the field. While recent advances in machine learning and…
Secondary structure plays an important role in determining the function of non-coding RNAs. Hence, identifying RNA secondary structures is of great value to research. Computational prediction is a mainstream approach for predicting RNA…
Predicting the secondary structure of RNA is a core challenge in computational biology, essential for understanding molecular function and designing novel therapeutics. The field has evolved from foundational but accuracy-limited…
No existing algorithm can start with arbitrary RNA sequences and return the precise, three-dimensional structures that ensures their biological function. This chapter outlines current algorithms for automated RNA structure prediction…
Due to the hierarchical organization of RNA structures and their pivotal roles in fulfilling RNA functions, the formation of RNA secondary structure critically influences many biological processes and has thus been a crucial research topic.…
Non-coding RNAs are ubiquitous, but the discovery of new RNA gene sequences far outpaces research on their structure and functional interactions. We mine the evolutionary sequence record to derive precise information about function and…
RNA's diverse biological functions stem from its structural versatility, yet accurately predicting and designing RNA sequences given a 3D conformation (inverse folding) remains a challenge. Here, I introduce a deep learning framework that…
Our work is concerned with the generation and targeted design of RNA, a type of genetic macromolecule that can adopt complex structures which influence their cellular activities and functions. The design of large scale and complex…
An RNA molecule is structured on several layers. The primary and most obvious structure is its sequence of bases, i.e. a word over the alphabet {A,C,G,U}. The higher structure is a set of one-to-one base-pairings resulting in a…
RNA structure and functional dynamics play fundamental roles in controlling biological systems. Molecular dynamics simulation, which can characterize interactions at an atomistic level, can advance the understanding on new drug discovery,…