Article
Biochemistry & Molecular Biology
Xiaoli Chen, Shaojie Zhang
Summary: The functions of non-coding RNAs are dependent on their 3D structures, making it critical to compare RNA 3D structures in order to analyze their functions. In this study, we identified a phenomenon where two non-coding RNAs may have similar substructures when their sequence order is rotated. To address this, we developed a software tool called CircularSTAR3D to detect circular matched substructures in RNA 3D structures. Our computational experiments on a non-redundant RNA structure dataset revealed the ubiquity of circular matching. We also demonstrated the usefulness of CircularSTAR3D in detecting conserved substructures missed by regular alignment tools.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemical Research Methods
Tomasz Wozniak, Malgorzata Sajek, Jadwiga Jaruzelska, Marcin Piotr Sajek
Summary: RNAlign2D is a fast Python tool that converts RNA sequences to pseudo-amino acid sequences, aligns them with the multiple protein sequence alignment tool MUSCLE, and produces accurate results in a short time. The pseudo-amino acid substitution matrix approach used in RNAlign2D is applicable for virtually all protein aligners.
BMC BIOINFORMATICS
(2021)
Article
Chemistry, Multidisciplinary
Higor D. F. de Melo, Daiane S. Carvalho, Fernando Hallwass, Ulrich Sternberg, Armando Navarro-Vazquez
Summary: An acrylonitrile/dimethylacrylamide cross-linked polymer can be swollen in different imidazolium ionic liquids, allowing for the measurement of residual dipolar couplings by mechanically compressing the polymer gels inside an NMR tube. Conformational analysis of the 1-methyl-3-butyl-imidazolium (BMIM) cation can be performed by using the measured RDCs as restraints in time-averaged molecular dynamics.
CHEMICAL COMMUNICATIONS
(2023)
Review
Biochemistry & Molecular Biology
Chris P. Sarnowski, Maria Bikaki, Alexander Leitner
Summary: Cross-linking and mass spectrometry (XL-MS) workflows are increasingly popular for low-resolution structural studies of macromolecular complexes. Protein-protein XL-MS protocols are widely adopted, while protein-RNA XL-MS workflows are evolving rapidly.
Article
Biochemical Research Methods
Mujtahid Akon, Muntashir Akon, Mohimenul Kabir, M. Saifur Rahman, M. Sohel Rahman
Summary: This research focuses on developing an alignment-free framework for analyzing biological sequences and introduces the Alignment-free Dissimilarity Analysis & Comparison Tool (ADACT), which aims to simplify the workflow for researchers and practitioners in the field of bioinformatics.
Article
Biochemical Research Methods
Maria Nattestad, Robert Aboukhalil, Chen-Shan Chin, Michael C. Schatz
Summary: Ribbon is a visualization tool that shows the positioning of alignments in both the reference genome and read contexts, providing an intuitive view to better understand structural variants and their supporting read evidence. It was developed to curate complex structural variant calls and determine if they are well supported by long-read evidence, using the same intuitive visualization method for genome-to-genome comparisons.
Article
Biochemistry & Molecular Biology
Bankala Krishnarjuna, Thirupathi Ravula, Edgar M. Faison, Marco Tonelli, Qi Zhang, Ayyalusamy Ramamoorthy
Summary: In this study, polymer-based nanodiscs were used to measure RDCs from nucleic acids. The nanodiscs were characterized and their alignment stability was confirmed. RDCs from a labeled nucleic acid molecule were successfully measured using the aligned nanodiscs. This demonstrates the potential of SMA-EA-based lipid-nanodiscs for structural and dynamical studies of nucleic acids.
Article
Biochemistry & Molecular Biology
Kez Cleal, Duncan M. Baird
Summary: Structural variation (SV) is important in genome evolution and disease, and Dysgu is a tool that accurately detects SVs using paired-end or long-read sequencing, with high sensitivity and fast running speed.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Mirjana M. Maljkovic, Nenad S. Mitic, Alexandre G. de Brevern
Summary: This study focuses on predicting Protein Blocks (PBs) from amino acid sequences using different data mining approaches and machine learning algorithms. The constructed models show varying importance of input attributes among algorithms. Utilizing information about amino acids in intrinsically disordered regions and repeats can improve the prediction accuracy for some PBs.
Article
Chemistry, Multidisciplinary
Ji Hwan Moon, Minsik Oh
Summary: Comprehensive analysis of gene expression data is essential for understanding condition-specific biological mechanisms from RNA-seq data. However, this often requires computational expertise, limiting accessibility to data analysis. To address this issue, TFNetPropX is introduced as an easy-to-use web-based platform that enables gene-level, gene-set-level, and network-level analysis of RNA-seq data under different conditions. The system predicts TF-affected genes and provides interactive web-based visualization of the results. Analysis on two TF knockout RNA-seq datasets demonstrates the utility of the system.
APPLIED SCIENCES-BASEL
(2023)
Article
Biochemical Research Methods
Alexis Dereeper, Marilyne Summo, Damien F. Meyer
Summary: PanExplorer is a web application that provides various genomic analyses and reports, aiding in the better understanding of bacterial pan-genomes.
Article
Biochemistry & Molecular Biology
Adam Osinski, Miles H. Black, Krzysztof Pawlowski, Zhe Chen, Yang Li, Vincent S. Tagliabracci
Summary: Studies reveal that Legionella effectors SidJ and its homolog SdjA adopt a kinase fold to regulate the activity of SidE ligases through glutamylation reaction, uncovering the structural and mechanistic basis in which the kinase fold catalyzes non-ribosomal amino acid ligations.
Article
Biochemistry & Molecular Biology
Gerard Minuesa, Cristina Alsina, Juan Antonio Garcia-Martin, Juan Carlos Oliveros, Ivan Dotu
Summary: MoiRNAiFold is a versatile and user-friendly tool for de novo synthetic RNA design, based on Constraint Programming, with the ability to handle multiple design constraints and quality measures, and improve features for RNA regulation control of gene expression. Demonstrated to outperform any previous software in benchmarking structural RNA puzzles from EteRNA.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemical Research Methods
Xiangyun Qiu
Summary: By quantitatively studying the performance and generalizability of a series of deep learning models, it is found that model generalizability rapidly degrades as sequence similarity decreases. The dependencies between generalizability and sequence and structure identity scores are further quantitated via pairwise alignment. The insights gained from this study provide valuable guidelines for deploying deep learning models in practice and advocate RNA secondary structure as a unique platform for developing generalizable learning-based models.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Nihad A. M. Al-Rashedi, Hussein Alburkat, Abas Hadi, Murad Munahi, Ali Jasim, Alaa Hameed, Basel Saber Oda, Kareem Moamin Lilo, Laith A. H. AlObaidi, Olli Vapalahti, Tarja Sironen, Teemu Smura
Summary: Since the first reported case of COVID-19 in China, SARS-CoV-2 has been spreading globally. Genomic surveillance plays a crucial role in tracking the emergence, introduction, and spread of new variants. The rapid increase in COVID-19 infections in Iraq during the second wave is attributed to the introduction of concern variants, likely imported from Europe. Molecular epidemiological analysis revealed the dominance of the B.1.1.7 lineage in Iraq, with multiple strains closely related to those from European countries. A notable frequency of stop codon mutation was observed among the B.1.1.7 lineage sequences, but it didn't significantly affect the function of NS7a protein.
