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 …

Aptamer bioinformatics

AB Kinghorn, LA Fraser, S Liang, SCC Shiu… - International journal of …, 2017 - mdpi.com
Aptamers are short nucleic acid sequences capable of specific, high-affinity molecular
binding. They are isolated via SELEX (Systematic Evolution of Ligands by Exponential …

Web 3DNA 2.0 for the analysis, visualization, and modeling of 3D nucleic acid structures

S Li, WK Olson, XJ Lu - Nucleic acids research, 2019 - academic.oup.com
Abstract Web 3DNA (w3DNA) 2.0 is a significantly enhanced version of the widely used
w3DNA server for the analysis, visualization, and modeling of 3D nucleic-acid-containing …

SASBDB: Towards an automatically curated and validated repository for biological scattering data

AG Kikhney, CR Borges, DS Molodenskiy… - Protein …, 2020 - Wiley Online Library
Small‐angle scattering (SAS) of X‐rays and neutrons is a fundamental tool to study the
nanostructural properties, and in particular, biological macromolecules in solution. In …

The HADDOCK web server for data-driven biomolecular docking

SJ De Vries, M Van Dijk, AMJJ Bonvin - Nature protocols, 2010 - nature.com
Computational docking is the prediction or modeling of the three-dimensional structure of a
biomolecular complex, starting from the structures of the individual molecules in their free …

Cryo-EM structures of PRC2 simultaneously engaged with two functionally distinct nucleosomes

S Poepsel, V Kasinath, E Nogales - Nature structural & molecular …, 2018 - nature.com
Epigenetic regulation is mediated by protein complexes that couple recognition of chromatin
marks to activity or recruitment of chromatin-modifying enzymes. Polycomb repressive …

Structure of SWI/SNF chromatin remodeller RSC bound to a nucleosome

FR Wagner, C Dienemann, H Wang, A Stützer… - Nature, 2020 - nature.com
Chromatin-remodelling complexes of the SWI/SNF family function in the formation of
nucleosome-depleted, transcriptionally active promoter regions (NDRs),. In the yeast …

Structure of promoter-bound TFIID and model of human pre-initiation complex assembly

RK Louder, Y He, JR López-Blanco, J Fang, P Chacón… - Nature, 2016 - nature.com
The general transcription factor IID (TFIID) plays a central role in the initiation of RNA
polymerase II (Pol II)-dependent transcription by nucleating pre-initiation complex (PIC) …

Structure of the processive human Pol δ holoenzyme

C Lancey, M Tehseen, VS Raducanu, F Rashid… - Nature …, 2020 - nature.com
In eukaryotes, DNA polymerase δ (Pol δ) bound to the proliferating cell nuclear antigen
(PCNA) replicates the lagging strand and cooperates with flap endonuclease 1 (FEN1) to …

Effects of cytosine modifications on DNA flexibility and nucleosome mechanical stability

TTM Ngo, J Yoo, Q Dai, Q Zhang, C He… - Nature …, 2016 - nature.com
Cytosine can undergo modifications, forming 5-methylcytosine (5-mC) and its oxidized
products 5-hydroxymethylcytosine (5-hmC), 5-formylcytosine (5-fC) and 5-carboxylcytosine …