Aptamer–protein interactions: from regulation to biomolecular detection

C Ji, J Wei, L Zhang, X Hou, J Tan, Q Yuan… - Chemical …, 2023 - ACS Publications
Serving as the basis of cell life, interactions between nucleic acids and proteins play
essential roles in fundamental cellular processes. Aptamers are unique single-stranded …

Computational tools for aptamer identification and optimization

D Sun, M Sun, J Zhang, X Lin, Y Zhang, F Lin… - TrAC Trends in …, 2022 - Elsevier
Aptamers are single-stranded DNA or RNA oligonucleotides that can selectively bind to a
specific target. They are generally obtained by SELEX, but the procedure is challenging and …

Accurate prediction of protein–nucleic acid complexes using RoseTTAFoldNA

M Baek, R McHugh, I Anishchenko, H Jiang, D Baker… - Nature …, 2024 - nature.com
Protein–RNA and protein–DNA complexes play critical roles in biology. Despite
considerable recent advances in protein structure prediction, the prediction of the structures …

The HDOCK server for integrated protein–protein docking

Y Yan, H Tao, J He, SY Huang - Nature protocols, 2020 - nature.com
Abstract The HDOCK server (http://hdock. phys. hust. edu. cn/) is a highly integrated suite of
homology search, template-based modeling, structure prediction, macromolecular docking …

HDOCK: a web server for protein–protein and protein–DNA/RNA docking based on a hybrid strategy

Y Yan, D Zhang, P Zhou, B Li… - Nucleic acids research, 2017 - academic.oup.com
Protein–protein and protein–DNA/RNA interactions play a fundamental role in a variety of
biological processes. Determining the complex structures of these interactions is valuable, in …

Delicate structural coordination of the Severe Acute Respiratory Syndrome coronavirus Nsp13 upon ATP hydrolysis

Z Jia, L Yan, Z Ren, L Wu, J Wang, J Guo… - Nucleic acids …, 2019 - academic.oup.com
To date, an effective therapeutic treatment that confers strong attenuation toward
coronaviruses (CoVs) remains elusive. Of all the potential drug targets, the helicase of CoVs …

Induction of tumor apoptosis through a circular RNA enhancing Foxo3 activity

WW Du, L Fang, W Yang, N Wu, FM Awan… - Cell death & …, 2017 - nature.com
Circular RNAs are a class of non-coding RNAs that are receiving extensive attention.
Despite reports showing circular RNAs acting as microRNA sponges, the biological …

A circular RNA circ-DNMT1 enhances breast cancer progression by activating autophagy

WW Du, W Yang, X Li, FM Awan, Z Yang, L Fang, J Lyu… - Oncogene, 2018 - nature.com
Circular RNAs are a large group of noncoding RNAs that are widely expressed in
mammalian cells. Genome-wide analyses have revealed abundant and evolutionarily …

Nuclear genome-derived circular RNA circPUM1 localizes in mitochondria and regulates oxidative phosphorylation in esophageal squamous cell carcinoma

W Gong, J Xu, Y Wang, Q Min, X Chen… - … and Targeted Therapy, 2022 - nature.com
Circular RNAs (circRNAs) were shown to play an important role in the occurrence and
progression of tumors. However, the functions of nuclear genome-derived circRNAs …

RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme

Z Miao, RW Adamiak, M Antczak, RT Batey, AJ Becka… - Rna, 2017 - rnajournal.cshlp.org
RNA-Puzzles is a collective experiment in blind 3D RNA structure prediction. We report here
a third round of RNA-Puzzles. Five puzzles, 4, 8, 12, 13, 14, all structures of riboswitch …