Results 91 to 100 of about 14,795 (267)

RNA secondary structure prediction from multi-aligned sequences [PDF]

, 2013
It has been well accepted that the RNA secondary structures of most functional non-coding RNAs (ncRNAs) are closely related to their functions and are conserved during evolution.
A Balik, A Pauli, A Wilm, A Wilm, AC Penn, AR Gruber, AS Richter, B Knudsen, B Knudsen, C Witwer, CB Do, D Jager, D Sankoff, D Wei, DH Mathews, DH Mathews, E Bindewald, E Freyhult, E Rivas, EJ Meer, H Kiryu, H Yonemoto, IA Qureshi, IL Hofacker, IL Hofacker, IV Novikova, J Ruan, J Spirollari, JG Underwood, JM Watts, JR Proctor, JS McCaskill, JT Low, K Katoh, K Sato, K Sato, K Sato, KM Wong, LE Carvalho, M Andronescu, M Andronescu, M Esteller, M Hamada, M Hamada, M Hamada, M Hamada, M Hamada, M Hamada, M Hamada, M Hamada, M Kertesz, ME Nebel, MS Andronescu, P Ge, PP Gardner, PS Pang, R Luck, RD Dowell, RJ Klein, S Washietl, S Washietl, S Washietl, S Washietl, SE Seemann, SE Seemann, SH Bernhart, SM Sahraeian, SW Burge, T Puton, T Xia, Y Kato, Z Sukosd   +71 more
core   +1 more source

Nop9 binds the central pseudoknot region of 18S rRNA

Nucleic Acids Research, 2017
The assembly of eukaryotic ribosomes requires numerous factors that transiently associate with evolving pre-ribosomal particles. The Pumilio repeat-containing protein Nop9 briefly associates with the 90S pre-ribosome during its co-transcriptional ...
B. Wang, K. Ye
semanticscholar   +1 more source

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

Impact of the yeast S0/uS2-cluster ribosomal protein rpS21/eS21 on rRNA folding and the architecture of small ribosomal subunit precursors.

PLoS ONE, 2023
RpS0/uS2, rpS2/uS5, and rpS21/eS21 form a cluster of ribosomal proteins (S0-cluster) at the head-body junction near the central pseudoknot of eukaryotic small ribosomal subunits (SSU). Previous work in yeast indicated that S0-cluster assembly is required
Gisela Pöll, Joachim Griesenbeck, Herbert Tschochner, Philipp Milkereit   +3 more
doaj   +1 more source

Paradigms for computational nucleic acid design [PDF]

, 2004
The design of DNA and RNA sequences is critical for many endeavors, from DNA nanotechnology, to PCR‐based applications, to DNA hybridization arrays.
Dirks, Robert M., Lin, Milo, Pierce, Niles A., Winfree, Erik   +3 more
core   +5 more sources

Practical Outcomes From CASP16 for Users in Need of Biomolecular Structure Prediction

Proteins: Structure, Function, and Bioinformatics, Volume 94, Issue 1, Page 435-446, January 2026.
ABSTRACT The 16th Critical Assessment of Structure Prediction benchmarked advancements in biomolecular modeling, particularly in the context of AlphaFold 2 and 3 systems. Protein monomer and domain prediction is largely solved, with barely any space for further improvements at the backbone level except for very specific details, irregular secondary ...
Luciano A. Abriata, Matteo Dal Peraro
wiley   +1 more source

PseudoBase: a database with RNA pseudoknots [PDF]

Nucleic Acids Research, 2000
PseudoBase is a database containing structural, functional and sequence data related to RNA pseudo-knots. It can be reached at http://wwwbio. Leiden Univ.nl/ approximately Batenburg/PKB.html. This page will direct the user to a retrieval page from where a particular pseudoknot can be chosen, or to a submission page which enables the user to add ...
F H, van Batenburg, A P, Gultyaev, C W, Pleij, J, Ng, J, Oliehoek   +4 more
openaire   +2 more sources

The IRES5′UTR of the dicistrovirus cricket paralysis virus is a type III IRES containing an essential pseudoknot structure

Nucleic Acids Research, 2017
Cricket paralysis virus (CrPV) is a dicistrovirus. Its positive-sense single-stranded RNA genome contains two internal ribosomal entry sites (IRESs). The 5′ untranslated region (5′UTR) IRES5′UTR mediates translation of non-structural proteins encoded by ...
Lauriane Gross, Q. Vicens, Evelyne Einhorn, Audrey Noireterre, L. Schaeffer, L. Kuhn, J. Imler, G. Eriani, C. Meignin, F. Martin   +9 more
semanticscholar   +1 more source

YTHDC1 Orchestrates Telomerase Assembly via Scaffold‐Mediated TERT‐TERC Interaction

Aging Cell, Volume 25, Issue 1, January 2026.
Schematic illustration of the major findings: METTL3‐deposited m6A modifications on TERC recruit the reader protein YTHDC1, which functions as a molecular scaffold to facilitate telomerase holoenzyme assembly by bridging TERT to m6A‐modified TERC transcripts, thereby promoting the proliferation of AECs.
Xiaolei Cheng, Shixing Wang, Yanan Yu, Jianhang Xu, Qian Wang, Yuzhu Wei, Zeming Jin, Xinkun Qi, Dongdong Jian, Yingchao Shi, Zhen Li, Zhengliang Ma, Wengong Wang, Tianjiao Xia, Junyue Xing, Xiaoping Gu, Hao Tang   +16 more
wiley   +1 more source

Pseudoknots in RNA secondary structures

Proceedings of the fourth annual international conference on Computational molecular biology, 2000
<p>RNA molecules are sequences of nucleotides that serve as more than mere intermediaries between DNA and proteins, e.g. as catalytic molecules. Computational prediction of RNA secondary structure is among the few structure prediction problems that can be solved satisfactorily in polynomial time. Most work has been done to predict structures that
Rune B. Lyngsø, Christian N. S. Pedersen   +1 more
openaire   +2 more sources