In-silico selection of aptamer: A review on the revolutionary approach to understand the aptamer design and interaction through computational chemistry

MZ Sabri, AAA Hamid, SMS Hitam… - Materials Today …, 2019 - Elsevier
… the computational time spent through RNA aptamers selection approach … aptamer screening,
Rabal O., and co-workers[17] proposed a workflow starting from the designing of aptamers

In silico approaches to RNA aptamer design

M Hamada - Biochimie, 2018 - Elsevier
select candidate RNA aptamers that bind to a target protein with high affinity and specificity.
After candidate selection, … Specifically, several types of computational methods are described …

Computational tools for aptamer identification and optimization

D Sun, M Sun, J Zhang, X Lin, Y Zhang, F Lin… - TrAC Trends in …, 2022 - Elsevier
… tools at work, we also review recent advanced studies on in silico selection of aptamers
against SARS-CoV-2. This review will aid in the development and use of high-throughput, less …

In silico selection of RNA aptamers

Y Chushak, MO Stone - Nucleic acids research, 2009 - academic.oup.com
computational approach for designing a starting pool of RNA sequences for the selection of
RNA aptamers … Our approach consists of three steps: (i) selection of RNA sequences based …

Computational design of RNA libraries for in vitro selection of aptamers

YG Chushak, JA Martin, JL Chávez… - … : Methods and Protocols, 2014 - Springer
… a random library of RNA sequences, and many aptamers selected from such random
pools … We present here a computational approach for designing a starting library of RNA

Computational approaches toward the design of pools for the in vitro selection of complex aptamers

X Luo, M McKeague, S Pitre, M Dumontier, J Green… - Rna, 2010 - rnajournal.cshlp.org
… in RNA/DNA pools, and Genetic Filtering designs RNA/DNA pools to a specified structure
distribution, whether uniform or otherwise. We show that using our computationally … to select for …

AptCompare: optimized de novo motif discovery of RNA aptamers via HTS-SELEX

KR Shieh, C Kratschmer, KE Maier, JM Greally… - …, 2020 - academic.oup.com
… of RNA aptamer motifs and uses a simple weighted ranking to order the candidate aptamers,
… the top-ranked candidate aptamers from a previously published selection experiment in our …

Computational predictive approaches for interaction and structure of aptamers

N Emami, PS Pakchin, R Ferdousi - Journal of Theoretical Biology, 2020 - Elsevier
… for effective aptamer selection and designing … computational predictive approaches of the
aptamer has been organized. Generally, the computational prediction approaches of aptamer

Computational Selection of RNA Aptamer against Angiopoietin‐2 and Experimental Evaluation

WP Hu, JV Kumar, CJ Huang… - BioMed research …, 2015 - Wiley Online Library
… -protein interactions by using the ZDOCK scoring function is that the RNA aptamers used in
RNA aptamer sequences were generated from three reference structures of aptamers, and …

Structural computational modeling of RNA aptamers

X Xu, DD Dickey, SJ Chen, PH Giangrande - Methods, 2016 - Elsevier
… of long RNA sequences and the slow post-selection … In a recent study we used computational
RNA structural and RNA/… membrane antigen (PSMA) RNA aptamer (70 nucleotides long) […