ArticleJournal of computer-aided molecular design2015
Computational docking simulations of a DNA-aptamer for argininamide and related ligands.
Article in Journal of computer-aided molecular design, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Characterization of the Specific Binding Between Aptamers and Cytochrome c With Pressure-Assisted Capillary Electrophoresis Frontal Analysis.Electrophoresis · 2025Article
- Surface-Modified Nanozymes for Enhanced and Selective Catalysis.ACS applied materials & interfaces · 2025Review
- Aptamer-based approaches in leukemia: a paradigm shift in targeted therapy.Clinical and experimental medicine · 2025Review
- Establishing Detection Methods for Okadaic Acid Aptamer-Target Interactions: Insights from Computational and Experimental Approaches.Foods (Basel, Switzerland) · 2025Article
- Systematic bio-fabrication of aptamers and their applications in engineering biology.Systems microbiology and biomanufacturing · 2023Review
- Aptamer-Protein Structures Guide In Silico and Experimental Discovery of Aptamer-Short Peptide Recognition Complexes or Aptamer-Amino Acid Cluster Complexes.The journal of physical chemistry. B · 2022Article
- Engineering constructed of high selectivity dexamethasone aptamer based on truncation and mutation technology.Frontiers in bioengineering and biotechnology · 2022Article
- Aptamer-Functionalized Hybrid Nanostructures for Sensing, Drug Delivery, Catalysis and Mechanical Applications.International journal of molecular sciences · 2021Review
- Methods and Applications of In Silico Aptamer Design and Modeling.International journal of molecular sciences · 2020Review
- Docking Simulation and Sandwich Assay for Aptamer-Based Botulinum Neurotoxin Type C Detection.Biosensors · 2020Article
- Article
- Beacons Contribute Valuable Empirical Information to Theoretical 3-D Aptamer-Peptide Binding.Journal of fluorescence · 2019Article
- Potential Inherent Stimulation of the Innate Immune System by Nucleic Acid Aptamers and Possible Corrective Approaches.Pharmaceuticals (Basel, Switzerland) · 2018Review
- Simple Methods and Rational Design for Enhancing Aptamer Sensitivity and Specificity.Frontiers in molecular biosciences · 2018Article
- Rational design of supramolecular hemin/G-quadruplex-dopamine aptamer nucleoapzyme systems with superior catalytic performance.Chemical science · 2016Article
- Improved Homology Model of the Human all-trans Retinoic Acid Metabolizing Enzyme CYP26A1.Molecules (Basel, Switzerland) · 2016Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The binding properties of sequence-specific nucleic acids (aptamers) to low-molecular-weight ligands, macromolecules and even cells attract substantial scientific interest. These ligand-DNA complexes found different applications for sensing, nanomedicine, and DNA nanotechnology. Structural information on the aptamer-ligand complexes is, however, scarce, even though it would open-up the possibilities to design novel features in the complexes. In the present study we apply molecular docking simulations to probe the features of an experimentally documented L-argininamide aptamer complex. The docking simulations were performed using AutoDock 4.0 and YASARA Structure software, a well-suited program for following intermolecular interactions and structures of biomolecules, including DNA. We explored the binding features of a DNA aptamer to L-argininamide and to a series of arginine derivatives or arginine-like ligands. We find that the best docking results are obtained after an energy-minimization of the parent ligand-aptamer complexes. The calculated binding energies of all mono-substituted guanidine-containing ligands show a good correlation with the experimentally determined binding constants. The results provide valuable guidelines for the application of docking simulations for the prediction of aptamer-ligand structures, and for the design of novel features of ligand-aptamer complexes.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.