Article
Virology
Han Wan, Rebecca L. Adams, Brett D. Lindenbach, Anna Marie Pyle
Summary: Researchers have reported a complete secondary structure map of the HCV RNA genome, revealing its folding in the cellular context and demonstrating the importance of many structures in the virus life cycle. Furthermore, this work provides a resource for future studies aimed at identifying therapeutic targets and conducting further mechanistic studies on this important human pathogen.
JOURNAL OF VIROLOGY
(2022)
Article
Genetics & Heredity
Gongwang Yu, Hanbing Zhu, Xiaoshu Chen, Jian-Rong Yang
Summary: The study investigates the secondary structure characteristics of mRNAs and their importance in function and evolution. It is found that specific folding of mRNAs may be an adaptive trait associated with important genes or sites, potentially providing the advantage of modulating ribosome movement. This reveals a novel aspect of the RNA structurome with functional and evolutionary implications.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2021)
Article
Biochemical Research Methods
Chun-Chi Chen, Yi-Ming Chan
Summary: In this paper, a deep learning-based method called REDfold is proposed for RNA secondary structure prediction. The method utilizes a CNN-based encoder-decoder network to learn the dependencies between RNA sequences and employs symmetric skip connections to efficiently propagate activation information. Additionally, the network output is post-processed with constrained optimization for accurate predictions, even for RNAs with pseudoknots. Experimental results demonstrate that REDfold outperforms contemporary state-of-the-art methods in terms of efficiency and accuracy.
BMC BIOINFORMATICS
(2023)
Article
Multidisciplinary Sciences
Makiha Fukuda, Jitong Cai, Joel S. Bader, Jef D. Boeke
Summary: A synthetic biology approach to constructing an RNA-based genome expands our understanding of living things and opens avenues for technological advancement. Understanding the structure-function relationships of RNA sequences is critical for the precise design of an artificial RNA replicon.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemical Research Methods
Vo Hong Thanh, Dani Korpela, Pekka Orponen
Summary: The study proposes a kinetic model for RNA folding process that takes into account cotranscriptional effects, which can predict favored conformations in actual biological systems. The computational tool developed in the study offers valuable insights into the kinetics of RNA folding.
JOURNAL OF COMPUTATIONAL BIOLOGY
(2021)
Article
Biophysics
Gianmarco Lazzeri, Cristian Micheletti, Samuela Pasquali, Pietro Faccioli
Summary: By applying an enhanced path-sampling method to RNA, we successfully simulate the folding process and resolve the challenges of developing realistic force fields and sampling rare conformational transitions. The folding landscape of RNA is found to be more frustrated compared to small proteins with similar size and architecture. The predicted folding mechanisms of RNA are consistent with experiments and existing models. This method provides a promising platform to accurately study atomistic RNA folding trajectories and preserve sequence information.
BIOPHYSICAL JOURNAL
(2023)
Article
Biochemical Research Methods
Daniele Marchei, Emanuela Merelli
Summary: In this paper, the authors extend the tangle-based model of RNA secondary structures and analyze patterns using prime factorizations. By mapping RNA to tangles, they demonstrate that the prime factorizations of tangles share similarities with RNA folding features. The authors also discuss future research directions and propose practical applications of the tangle-based method for RNA classification and folding prediction, despite the incomplete factorization.
BMC BIOINFORMATICS
(2022)
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
Biochemistry & Molecular Biology
Anna A. Mikkelsen, Feng Gao, Elizabeth Carino, Sayanta Bera, Anne E. Simon
Summary: Plus-strand RNA viruses often use -1 programmed ribosomal frameshifting to maximize their coding capacity. This study discovered six tertiary interactions associated with the FSE of citrus yellow vein associated virus, which covers three-quarters of the genomic RNA. Two long-distance interactions connect sequences on opposite sides of the critical FSE central stem, destabilizing the FSE and potentially allowing ribosome progression through a disrupted upstream FSE.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemical Research Methods
Kevin Sutanto, Marcel Turcotte
Summary: Non-coding RNAs (ncRNAs) are transcribed RNA elements that do not code for proteins but play important roles in biological processes and disorders. Their structure is closely associated with their functions and conservation. This study proposes the use of secondary structure fingerprints to improve classification accuracy by considering global and local structural matches. By combining these fingerprints with k-mers, a deep learning architecture achieved high accuracy, precision, and recall.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2023)
Article
Computer Science, Information Systems
Md Shahidul Islam, Md Rafiqul Islam
Summary: In this paper, the authors investigated the RNA structure prediction problem with pseudoknots. They used genetic algorithm, simulated annealing, and their combination to predict RNA secondary structure. Through comparisons on five datasets, the combination of genetic algorithm and simulated annealing demonstrated the best performance.
JOURNAL OF KING SAUD UNIVERSITY-COMPUTER AND INFORMATION SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Sicheng Zhang, Yi Cheng, Peixuan Guo, Shi-Jie Chen
Summary: This article presents the VfoldMCPX model, a new model for predicting the structure and folding stability of multistrand RNA complexes, including those containing pseudoknots. Extensive testing shows that the model provides improved accuracy for multistranded RNA complexes.
Article
Biochemical Research Methods
Sumit Mukherjee, Matan Drory Retwitzer, Sara M. Hubbell, Michelle M. Meyer, Danny Barash
Summary: Riboswitches are conserved RNA sensors that mainly regulate genes/operons in bacteria. The challenge is to discover riboswitch classes in eukaryotes and understand the evolution of bacterial riboswitches. A novel approach based on inverse RNA folding was developed to identify potential structural candidates in fungi that could be distant homologs of bacterial riboswitches. This method transforms a structure-based search into a sequence-based search, considering the conservation of secondary structure shape and ligand-binding residues.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biochemistry & Molecular Biology
Evangelos Makris, Angelos Kolaitis, Christos Andrikos, Vrettos Moulos, Panayiotis Tsanakas, Christos Pavlatos
Summary: This paper aims to create a pioneering framework for predicting specific RNA structures, particularly focusing on H-type pseudoknots including bulges and internal loops. The proposed framework, Knotify+, leverages the power context-free grammar (CFG) along with maximum base pairing and minimum free energy to effectively address this ambiguous task. Knotify+ outperforms state-of-the-art frameworks in terms of accuracy in core stems prediction, providing higher accuracy in small sequences and comparable accuracy in larger ones, while requiring less execution time compared to well-known platforms.
Article
Chemistry, Physical
Jing-Jie Su, Xing-liang Xu, Ting-Ting Sun, Yu Shen, Yan Wang
Summary: By using a helix-based transition rate model and master equation, the study investigated the refolding and cotranscriptional folding processes of RNA pseudoknots, revealing differences in final states and intermediates between refolding and cotranscriptional folding. These findings provide insights into the cotranscription folding of hTR pseudoknot with different rates.
CHEMICAL PHYSICS LETTERS
(2021)
Article
Biochemical Research Methods
Mohamed Raef Smaoui, Henri Orland, Jerome Waldispuehl
Article
Mechanics
Satya N. Majumdar, Henri Orland
JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT
(2015)
Article
Multidisciplinary Sciences
Cristian Micheletti, Marco Di Stefano, Henri Orland
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2015)
Article
Biophysics
Guillaume Le Treut, Francois Kepes, Henri Orland
BIOPHYSICAL JOURNAL
(2016)
Article
Chemistry, Physical
Tomer Markovich, David Andelman, Henri Orland
JOURNAL OF CHEMICAL PHYSICS
(2016)
Article
Chemistry, Physical
Frederic Poitevin, Marc Delarue, Henri Orland
JOURNAL OF PHYSICAL CHEMISTRY B
(2016)
Editorial Material
Biochemistry & Molecular Biology
Aaron S. Burton, Marco Di Stefano, Niles Lehman, Henri Orland, Cristian Micheletti
Article
Chemistry, Physical
Xingkun Man, Kris T. Delaney, Michael C. Villet, Henri Orland, Glenn H. Fredrickson
JOURNAL OF CHEMICAL PHYSICS
(2014)
Article
Chemistry, Physical
Glenn H. Fredrickson, Henri Orland
JOURNAL OF CHEMICAL PHYSICS
(2014)
Article
Chemistry, Multidisciplinary
Patrice Koehl, Frederic Poitevin, Henri Orland, Marc Delarue
JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY
(2014)
Article
Biochemistry & Molecular Biology
Patrice Koehl, Henri Orland, Marc Delarue
Review
Virology
Yin-Chen Hsieh, Marc Delarue, Henri Orland, Patrice Koehl
Summary: The emergence of the COVID-19 pandemic has illustrated our vulnerability to novel viruses and zoonotic diseases. This paper reviews methods for analyzing structural information on large macromolecular systems and discusses three specific methods based on alpha shape theory, normal mode analyses, and modified Poisson-Boltzmann theories. Examples of their applications on the outer shells and structural proteins of the West Nile Virus are provided, demonstrating their compatibility with regular desktop computers.
Article
Computer Science, Artificial Intelligence
Patrice Koehl, Marc Delarue, Henri Orland
Summary: The Gromov-Wasserstein (GW) formalism is a generalization of the optimal transport (OT) formalism for comparing distributions in different metric spaces. Fast techniques based on entropy regularization have been developed to solve approximate GW problems, but numerical convergence issues remain. To address this, we propose a novel strategy using methods from statistical physics to solve the discrete GW problem. We demonstrate the accuracy and automaticity of our approach in non-rigid registration of shapes and provide numerical evidence for the correlation between low-resolution, surface-based representation of proteins and atomistic models.
Article
Computer Science, Artificial Intelligence
Patrice Koehl, Henri Orland
Summary: This algorithm computes nonrigid, possibly partial comparisons of shapes defined by unstructured triangulations of their surfaces. It finds a possibly partial correspondence between the vertices of two triangulations and measures the similarity of the shapes using a cost associated with this correspondence. The algorithm characterizes the vertices using signature vectors of features and computes the correspondence as the transport plan that solves the optimal transport or optimal partial transport problem between their sets of vertices using a statistical physics approach.
Article
Physics, Fluids & Plasmas
Graziano Vernizzi, Henri Orland, A. Zee
Article
Biochemistry & Molecular Biology
Ankita Chadda, Alexander G. Kozlov, Binh Nguyen, Timothy M. Lohman, Eric A. Galburt
Summary: In this study, it was found that the DNA damage response in Mycobacterium tuberculosis differs from well-studied model bacteria. The DNA repair helicase UvrD1 in Mtb is activated through a redox-dependent process and is closely associated with the homo-dimeric Ku protein. Additionally, Ku protein is shown to stimulate the helicase activity of UvrD1.
JOURNAL OF MOLECULAR BIOLOGY
(2024)