Results 21 to 30 of about 15,140,513 (376)

Rock, scissors, paper: How RNA structure informs function

The Plant Cell, 2023
RNA can fold back on itself to adopt a wide range of structures. These range from relatively simple hairpins to intricate 3D folds and can be accompanied by regulatory interactions with both metabolites and macromolecules.
S. Assmann, Hong-Li Chou, P. Bevilacqua
semanticscholar   +1 more source

Geometric deep learning of RNA structure

Science, 2021
Machine learning solves RNA puzzles RNA molecules fold into complex three-dimensional shapes that are difficult to determine experimentally or predict computationally.
Raphael J. L. Townshend, Stephan Eismann, A. Watkins, R. Rangan, Maria Karelina, Rhiju Das, R. Dror   +6 more
semanticscholar   +1 more source

Predicting RNA Structure with Vfold

Methods in molecular biology, 2017
Chenhan Zhao, Xiaojun Xu, Shi‐Jie Chen
openalex   +3 more sources

Integrating end-to-end learning with deep geometrical potentials for ab initio RNA structure prediction

bioRxiv, 2022
RNAs are fundamental in living cells and perform critical functions determined by the tertiary architectures. However, accurate modeling of 3D RNA structure remains a challenging problem.
Yang Li, Chengxin Zhang, Chen-Jie Feng, P. Freddolino, Yang Zhang   +4 more
semanticscholar   +1 more source

Deconstructing internal ribosome entry site elements: an update of structural motifs and functional divergences [PDF]

Open Biology, 2018
Beyond the general cap-dependent translation initiation, eukaryotic organisms use alternative mechanisms to initiate protein synthesis. Internal ribosome entry site (IRES) elements are cis-acting RNA regions that promote internal initiation of ...
Gloria Lozano, Rosario Francisco-Velilla, Encarnacion Martinez-Salas   +2 more
doaj   +1 more source

Topology of RNA-RNA Interaction Structures [PDF]

Journal of Computational Biology, 2012
40 pages 15 ...
Andersen, Jørgen E., Huang, Fenix W. D., Penner, Robert C., Reidys, Christian M.   +3 more
openaire   +6 more sources

Counting RNA Pseudoknotted Structures [PDF]

Journal of Computational Biology, 2011
In 2004, Condon and coauthors gave a hierarchical classification of exact RNA structure prediction algorithms according to the generality of structure classes that they handle. We complete this classification by adding two recent prediction algorithms. More importantly, we precisely quantify the hierarchy by giving closed or asymptotic formulas for the
Saule, Cédric, Regnier, Mireille, Steyaert, Jean-Marc, Denise, Alain   +3 more
openaire   +3 more sources

Cryo-EM advances in RNA structure determination

Signal Transduction and Targeted Therapy, 2022
Cryo-electron microscopy (cryo-EM) has emerged as an unprecedented tool to resolve protein structures at atomic resolution. Structural insights of biological samples not accessible by conventional X-ray crystallography and NMR can be explored with cryo ...
Haiyun Ma, Xin Jia, Kaiming Zhang, Zhaoming Su   +3 more
semanticscholar   +1 more source

Flexible pri-miRNA structures enable tunable production of 5’ isomiRs

RNA Biology, 2022
The Drosha cleavage of a pri-miRNA defines mature microRNA sequence. Drosha cleavage at alternative positions generates 5’ isoforms (isomiRs) which have distinctive functions. To understand how pri-miRNA structures influence Drosha cleavage, we performed
Xavier Bofill-De Ros, Zhenyi Hong, Ben Birkenfeld, Sarangelica Alamo-Ortiz, Acong Yang, Lisheng Dai, Shuo Gu   +6 more
doaj   +1 more source

RNA Secondary Structure Prediction [PDF]

Current Protocols in Nucleic Acid Chemistry, 2000
AbstractDetails for predicting secondary structure of RNA sequences using free energy minimization are given. Protocols present the use of the RNAstructure computer program (for PCs) and the mfold server (for Unix platforms). The minimum free energy structure and a set of suboptimal structures with similar free energies are predicted.
Mathews, David H., Turner, Douglas H., Zuker, Michael   +2 more
openaire   +5 more sources