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 …
specific target. They are generally obtained by SELEX, but the procedure is challenging and …
Aptamer bioinformatics
Aptamers are short nucleic acid sequences capable of specific, high-affinity molecular
binding. They are isolated via SELEX (Systematic Evolution of Ligands by Exponential …
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
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 …
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 …
nanostructural properties, and in particular, biological macromolecules in solution. In …
The HADDOCK web server for data-driven biomolecular docking
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 …
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 …
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 …
nucleosome-depleted, transcriptionally active promoter regions (NDRs),. In the yeast …
Structure of promoter-bound TFIID and model of human pre-initiation complex assembly
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) …
polymerase II (Pol II)-dependent transcription by nucleating pre-initiation complex (PIC) …
Structure of the processive human Pol δ holoenzyme
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 …
(PCNA) replicates the lagging strand and cooperates with flap endonuclease 1 (FEN1) to …
Effects of cytosine modifications on DNA flexibility and nucleosome mechanical stability
Cytosine can undergo modifications, forming 5-methylcytosine (5-mC) and its oxidized
products 5-hydroxymethylcytosine (5-hmC), 5-formylcytosine (5-fC) and 5-carboxylcytosine …
products 5-hydroxymethylcytosine (5-hmC), 5-formylcytosine (5-fC) and 5-carboxylcytosine …