Results 91 to 100 of about 12,203 (191)

Functional Relevance of CASP16 Nucleic Acid Predictions as Evaluated by Structure Providers

Proteins: Structure, Function, and Bioinformatics, Volume 94, Issue 1, Page 51-78, January 2026.
ABSTRACT Accurate biomolecular structure prediction enables the prediction of mutational effects, the speculation of function based on predicted structural homology, the analysis of ligand binding modes, experimental model building, and many other applications.
Rachael C. Kretsch, Reinhard Albrecht, Ebbe S. Andersen, Hsuan‐Ai Chen, Wah Chiu, Rhiju Das, Jeanine G. Gezelle, Marcus D. Hartmann, Claudia Höbartner, Yimin Hu, Shekhar Jadhav, Philip E. Johnson, Christopher P. Jones, Deepak Koirala, Emil L. Kristoffersen, Eric Largy, Anna Lewicka, Cameron D. Mackereth, Marco Marcia, Michela Nigro, Manju Ojha, Joseph A. Piccirilli, Phoebe A. Rice, Heewhan Shin, Anna‐Lena Steckelberg, Zhaoming Su, Yoshita Srivastava, Liu Wang, Yuan Wu, Jiahao Xie, Nikolaj H. Zwergius, John Moult, Andriy Kryshtafovych   +32 more
wiley   +1 more source

Structure and ligand binding of the glutamine-II riboswitch [PDF]

, 2019
We have determined the structure of the glutamine-II riboswitch ligand binding domain using X-ray crystallography. The structure was solved using a novel combination of homology modeling and molecular replacement.
Das, Rhiju, Huang, Lin, Lilley, David M. J., Wang, Jia, Watkins, Andrew M.   +4 more
core   +2 more sources

Riboswitches as hormone receptors: hypothetical cytokinin-binding riboswitches in Arabidopsis thaliana [PDF]

Biology Direct, 2010
Riboswitches are mRNA elements that change conformation when bound to small molecules. They are known to be key regulators of biosynthetic pathways in both prokaryotes and eukaryotes.The hypothesis presented here is that riboswitches function as receptors in hormone perception.
Downes Brian, Grojean Jeremy
openaire   +3 more sources

The RNA‐Puzzles Assessments of RNA‐Only Targets in CASP16

Proteins: Structure, Function, and Bioinformatics, Volume 94, Issue 1, Page 218-229, January 2026.
ABSTRACT RNA‐Puzzles was launched in 2011 as a collaborative effort dedicated to advancing and improving RNA 3D structure prediction. The automatic evaluation protocols for comparisons between prediction and experiment developed within RNA‐Puzzles are applied to the 2024 CASP16 competition.
Eric Westhof, Hao Sun, Fan Bu, Zhichao Miao   +3 more
wiley   +1 more source

RiboMicrobe: An Integrated Translatome Atlas for Microorganism

Advanced Science, Volume 12, Issue 48, December 29, 2025.
RiboMicrobe is a comprehensive database for Ribo‐seq data from prokaryotes, featuring 891 Ribo‐seq, 369 RNA‐seq, and 62 proteome datasets from 38 species. The database not only provides various data visualization results but also includes two sORF prediction models and a suit of bioinformatics tools for comparative analysis, facilitating easy access ...
Yingshun Zhou, Jinjing Luo, Xiaoqiang Lang, Yuli Gan, Guoxian Liu, Yuling Cui, Fazhi Li, Weicong Zhu, Bing Chen, Yuanyuan Dong, Yinglin Wu, Yi Cao, Qi Liu   +12 more
wiley   +1 more source

Functional Analysis of Histidine‐Dependent Self‐Cleaving RNAs Obtained by In Vitro Selection

ChemBioChem, Volume 26, Issue 21, November 8, 2025.
Ribozymes can be nucleic acid medicines given their catalytic activity. We attempted to obtain functional RNAs that mimic ribonuclease A catalytic mechanisms. Functional RNAs with high histidine specificity were obtained, suggesting that histidine acts in active structure formation.
Nae Sakimoto, Shoichiro Tanaka, Riki Hatakenaka, Yoshie Yamaguchi‐Miyazaki, Elisa Tomita‐Sudo, Tomoka Akita, Taku Ishigaki, Shigenori Iwai, Junji Kawakami   +8 more
wiley   +1 more source

Tb3+-Cleavage Assays Reveal Specific Mg2+ Binding Sites Necessary to Pre-fold the btuB Riboswitch for AdoCbl Binding [PDF]

, 2017
Riboswitches are RNA elements that bind specific metabolites in order to regulate the gene expression involved in controlling the cellular concentration of the respective molecule or ion.
Choudhary, Pallavi K, Gallo, Sofia, Sigel, Roland K O   +2 more
core   +1 more source

Riboswitches and Translation Control [PDF]

Cold Spring Harbor Perspectives in Biology, 2018
A growing collection of bacterial riboswitch classes is being discovered that sense central metabolites, coenzymes, and signaling molecules. Included among the various mechanisms of gene regulation exploited by these RNA regulatory elements are several that modulate messenger RNA (mRNA) translation. In this review, the mechanisms of riboswitch-mediated
openaire   +2 more sources

Riboswitching on RNA virus replication [PDF]

Proceedings of the National Academy of Sciences, 2007
Positive-strand RNA viruses direct different virus-specific processes during their infection of host cells. Fundamental events such as viral RNA genome replication are controlled by viral regulatory RNA elements (REs). Here, we have investigated the possibility of specifically modulating the action of a viral RE using RNA aptamer technology.
Sheng, Wang, K Andrew, White
openaire   +2 more sources

Consolidate Overview of Ribonucleic Acid Molecular Dynamics: From Molecular Movements to Material Innovations

Advanced Engineering Materials, Volume 27, Issue 22, November 2025.
Molecular dynamics simulations are advancing the study of ribonucleic acid (RNA) and RNA‐conjugated molecules. These developments include improvements in force fields, long‐timescale dynamics, and coarse‐grained models, addressing limitations and refining methods.
Kanchan Yadav, Iksoo Jang, Jong Bum Lee
wiley   +1 more source