Article
Biochemistry & Molecular Biology
Tzu-Hsien Yang, Yu-Cian Lin, Min Hsia, Zhan-Yi Liao
Summary: This research implemented a web service called SSRTool for ranking and evaluating predicted structures of a given sequence. Based on computed species-specific interpretability significance, SSRTool provides functions for ranking user-generated predictions, automated prediction and ranking for a given sequence, and inferring the functional aspects of a given structure.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Multidisciplinary Sciences
Quentin Vicens, Jeffrey S. Kieft
Summary: Recent events have brought RNA research into the spotlight, igniting a new passion for understanding the diverse functions and structure of RNA. However, there is a misunderstanding of the foundational characteristics of RNA structure, often viewed as a single floppy strand. The purpose of this article is to help adjust mental models, better utilize RNA structural information, and provide suggestions for future efforts.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Biochemical Research Methods
Kengo Sato, Michiaki Hamada
Summary: Computational analysis of RNA sequences plays a crucial role in RNA biology. In recent years, the incorporation of artificial intelligence and machine learning techniques into RNA sequence analysis has gained significant traction. Machine learning-based approaches have shown remarkable advancements, enhancing the precision of sequence analysis related to RNA secondary structures. Furthermore, artificial intelligence and machine learning innovations are also applied in the analysis of RNA-small molecule interactions, RNA drug discovery, and the design of RNA aptamers.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biochemistry & Molecular Biology
Margherita A. G. Matarrese, Alessandro Loppini, Martina Nicoletti, Simonetta Filippi, Letizia Chiodo
Summary: The study of RNA structure is crucial in understanding RNA molecular functioning. With the flexibility of RNA, the large number of expressed RNAs, and the diverse functions they have, it is difficult to obtain structural information on the same scale as is available for proteins. In silico prediction of RNA 3D structures is particularly important to understand the relationship between structure and function, as the 3D structure plays a significant role in molecular interactions with DNA or protein complexes. The accuracy of RNA 3D structure prediction relies on a properly predicted or measured secondary structure. This paper comparatively evaluates computational tools for modeling RNA secondary structure, focusing on freely available web-server versions for more accessible use. The evaluation focuses on the performance for long sequences and aims to select the best methods for investigating long non-coding RNAs (lncRNAs), which are of special relevance due to their involvement in regulatory mechanisms.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemical Research Methods
Vyacheslav Tretyachenko, Vaclav Voracek, Radko Soucek, Kosuke Fujishima, Klara Hlouchova
Summary: CoLiDe is a computational tool that offers precise control over protein sequence composition, length, and diversity for designing combinatorial libraries. It uses an evolutionary approach to provide solutions for degenerate DNA templates and can prepare purified protein library samples with up to 10^11 - 10^12 unique sequences. CoLiDe presents a composition-centric approach to protein design for different functional phenomena.
Article
Biochemical Research Methods
Kengo Sato, Yuki Kato
Summary: Pseudoknots are important RNA structural elements involved in various biological phenomena. Current methods for secondary structure prediction considering pseudoknots are not widely available. We propose an improved version of IPknot that enables linear time calculation and automatic selection of optimal threshold parameters.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemical Research Methods
Tzu-Hsien Yang
Summary: A novel method was proposed in this research to identify the functionally interpretable structure ensemble of a given RNA sequence and provide the meta-stable structure based on the ensemble. The method outperformed existing tools in predicting meta-stable structures and showed resistance to sequence length-dependent performance deterioration. The study demonstrated the importance of considering RNA structure ensembles for functional hypotheses.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Chia-Tzu Ho, Yu-Wei Huang, Teng-Ruei Chen, Chia-Hua Lo, Wei-Cheng Lo
Summary: Secondary structure prediction (SSP) of proteins is an important technique in structural biology with many applications. In the past seven decades, around 300 algorithms have been published, and the estimated limit of three-state SSP accuracy has been re-evaluated to be approximately 92%, while the limit for eight-state SSP is estimated to be in the range of 84-87%. This shows that SSP remains challenging and there is room for improvement in the field.
Article
Multidisciplinary Sciences
Ryan J. Andrews, Warren B. Rouse, Collin A. O'Leary, Nicholas J. Booher, Walter N. Moss
Summary: The identification of RNA elements in genomes and transcriptomes is a major challenge in target discovery for research and intervention. ScanFold 2.0, a revised version of the original algorithm, uses machine learning to estimate folding energy and significantly improves prediction speeds for large sequences. Comparative tests demonstrate the consistency and efficiency of ScanFold 2.0 compared to the original version.
Article
Virology
Simon Poblete, Horacio V. Guzman
Summary: Studying the three-dimensional reconstruction of RNA is crucial for understanding the functions of proteinaceus capsids, but RNA self-association remains an open question. Recent chemical probing reports provide reliable secondary structures of diverse RNA ensembles. The proposed method combines a coarse-grained model with a subdomain composition scheme to reconstruct the complete 3D structure of RNA genomes based on experimental techniques.
Article
Microbiology
Gaspar Bruner-Montero, Carlos M. M. Luque, Cassia Siqueira Cesar, Shuai Dominique Ding, Jonathan P. P. Day, Francis Michael Jiggins
Summary: By establishing infected insect cells and a simple virus detection method, we successfully isolated La Jolla virus and Newfield virus. These viruses have harmful effects on the host and can sterilize fruit flies, with potential for biocontrol of the crop pest Drosophila suzukii.
Article
Chemistry, Analytical
Omair Adil, Seth B. Eddington, Keith T. Gagnon, Mohtashim H. Shamsi
Summary: Overgrowth of short tandem repeat sequences in genes can cause neurodegenerative disorders. These repeat sequences are ideal targets for label-free electrochemical detection, but their secondary structures and sporadic repeats can complicate detection. By analyzing different nucleic acid microprobe backbones, the study found that the lock-nucleic acid (LNA) microprobe can specifically detect tandem repeats and perform better with the presence of Mg2+. The LNA-based platform shows potential for the development of a reliable biosensor for genetic neurodegenerative disorders.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Vaclav Brazda, Jan Havlik, Jan Kolomaznik, Oldrich Trenz, Jiri Stastny
Summary: R-loops, formed by RNA-DNA hybrid and displaced single-stranded DNA, are common non-B nucleic acid structures that play important roles in human diseases by promoting mutagenesis, hyper-recombination, and transcription-replication collisions. To better study and predict R-loops, researchers have developed the R-loop tracker tool, integrating it with other nucleic acids analysis tools and enhancing visualization outputs.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Hong Wang, Xiaoyan Lu, Hewei Zheng, Guosi Zhang, Siyu Wang, Peng Lin, Youyuan Zhuang, Chong Chen, Qi Chen, Jia Qu, Liangde Xu
Summary: RNA structure is crucial for gene regulation, stability, and biological processes. A strategy called RNA secondary-structural motif-comparing (RNAsmc) is presented to identify and evaluate structural motifs. RNAsmc is robust to sequence length, folding protocol, and RNA structural profile. It can also be used to quantify structural variation in RNA editing events. The findings show that RNAsmc can uncover RNA structural heterogeneity and cluster RNA families. Additionally, an R software package, RNAsmc, is available for download to explore, align, and cluster RNA secondary structures.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Multidisciplinary Sciences
He Zhang, Liang Zhang, Ang Lin, Congcong Xu, Ziyu Li, Kaibo Liu, Boxiang Liu, Xiaopin Ma, Fanfan Zhao, Huiling Jiang, Chunxiu Chen, Haifa Shen, Hangwen Li, David H. Mathews, Yujian Zhang, Liang Huang
Summary: mRNA vaccines against COVID-19 face challenges due to mRNA instability and degradation. A new algorithm, LinearDesign, finds optimal mRNA designs by optimizing both stability and codon usage. This design substantially improves mRNA half-life, protein expression, and antibody titre in mice.
