ReviewInternational journal of molecular sciences2020
Methods and Applications of In Silico Aptamer Design and Modeling.
Review in International journal of molecular sciences, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 61 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
61 citing papers in PubMed, 139 citations in OpenAlex.
- An electrochemical aptasensor for determining fumonisin BFood chemistry. Molecular sciences · 2026Article
- A Multi-Engine Consensus Docking Pipeline for RNA Aptamer Screening Against ACC Oxidase (ACO): Statistical Validation, Machine Learning Analysis, and Pilot Cross-Target Evaluation Against ACC Synthase (ACS).International journal of molecular sciences · 2026Article
- Article
- Targeting Undruggable Protein Interactions with DNA Aptamers: Inhibition of the Interaction BetweenInternational journal of molecular sciences · 2026Article
- Structure-guided development of an electrochemical aptasensor for Salmonella Typhi HlyE antigen detection using in silico and experimental approaches.Scientific reports · 2026Article
- Aptamer-Based Delivery of Genes and Drugs Across the Blood-Brain Barrier.Pharmaceuticals (Basel, Switzerland) · 2026Review
- BioMutation: a portable graphical user interface for mutagenesis and feature analysis in proteins, nucleic acids, and their complexes.Frontiers in genetics · 2026Article
- Review
- Spiegelmer Aptamers: Innovative Approach in Breast Cancer.Breast cancer : basic and clinical research · 2026Review
- Geniposide Inhibits Oral Squamous Cell Carcinoma by Regulating PI3K-Akt Signaling-Mediated Apoptosis: A Multi-Method Validation Study.Current issues in molecular biology · 2025Article
- Aptamer-Nanoconjugates as Potential Theranostics in Major Neuro-Oncological and Neurodegenerative Disorders.Pharmaceutics · 2025Review
- Aptamers as Potential Inhibitors of Ethylene Biosynthesis: Identification and In Silico Selection.International journal of molecular sciences · 2025Article
- A Cyanobacteria-Derived RNA Aptamer Resensitizes Prostate Cancer to Hormone Therapy.Cancer research · 2025Article
- Progress in Aptamer Research and Future Applications.ChemistryOpen · 2025Review
- Beyond traditional diagnosis: aptamer-based microRNA detection for the early diagnosis of periodontitis.Molecular biology reports · 2025Review
- Review
- Using aptamers for targeted delivery of RNA therapies.Molecular therapy : the journal of the American Society of Gene Therapy · 2025Review
- The 20th Anniversary of Pegaptanib (MacugenTM), the First Approved Aptamer Medicine: History, Recent Advances and Future Prospects of Aptamers in Therapy.Pharmaceutics · 2025Review
- Continuous Biosensing to Monitor Acute Systemic Inflammation, a Diagnostic Need for Therapeutic Guidance.ACS sensors · 2025Review
- Review
1 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
Aptamers are nucleic acid analogues of antibodies with high affinity to different targets, such as cells, viruses, proteins, inorganic materials, and coenzymes. Empirical approaches allow the design of in vitro aptamers that bind particularly to a target molecule with high affinity and selectivity. Theoretical methods allow significant expansion of the possibilities of aptamer design. In this study, we review theoretical and joint theoretical-experimental studies dedicated to aptamer design and modeling. We consider aptamers with different targets, such as proteins, antibiotics, organophosphates, nucleobases, amino acids, and drugs. During nucleic acid modeling and in silico design, a full set of in silico methods can be applied, such as docking, molecular dynamics (MD), and statistical analysis. The typical modeling workflow starts with structure prediction. Then, docking of target and aptamer is performed. Next, MD simulations are performed, which allows for an evaluation of the stability of aptamer/ligand complexes and determination of the binding energies with higher accuracy. Then, aptamer/ligand interactions are analyzed, and mutations of studied aptamers made. Subsequently, the whole procedure of molecular modeling can be reiterated. Thus, the interactions between aptamers and their ligands are complex and difficult to understand using only experimental approaches. Docking and MD are irreplaceable when aptamers are studied in silico.
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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.