ReviewMolecules (Basel, Switzerland)2020
How 'Protein-Docking' Translates into the New Emerging Field of Docking Small Molecules to Nucleic Acids?
Review in Molecules (Basel, Switzerland), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 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
19 citing papers in PubMed, 50 citations in OpenAlex.
- Exploring Secondary Structure Predictions for RNA-Targeted Drug Discovery: Power and Challenges.Journal of chemical information and modeling · 2026Article
- Chemical Profiling, Molecular Docking, and Mechanistic Anticancer Activity ofMolecules (Basel, Switzerland) · 2026Article
- Article
- RLDOCKScore: A Scoring Function for RNA-Ligand Docking and Small Molecule Virtual Screening.Journal of chemical theory and computation · 2025Article
- Naphthyridine carbamate dimer ligand induces formation of Z-RNA-like fold of disease-related RNA and exhibits a molecular glue characteristics in crystal lattice formation.Nucleic acids research · 2025Article
- Dissecting the function of the DNMT2-homolog (DNMA) in Dictyostelium discoideum.G3 (Bethesda, Md.) · 2025Article
- Overcoming translational barriers in RNA-protein docking: enhancing computational accuracy for targeted drug discovery.Future medicinal chemistry · 2025Review
- Investigating the molecular mechanisms of the "Astragalus-Codonopsis" herb pair in treating diabetes: a network pharmacology and bioinformatics approach with molecular docking validation.Frontiers in bioengineering and biotechnology · 2025Article
- Harnessing Computational Approaches for RNA-Targeted Drug Discovery.RNA nanomed · 2024Article
- Modeling and NMR Data Elucidate the Structure of a G-Quadruplex-Ligand Interaction for a Pu22T-Cyclometalated Iridium(III) System.The journal of physical chemistry. B · 2024Article
- Functionalized siRNA-chitosan nanoformulations promote triple-negative breast cancer cell death via blocking the miRNA-21/AKT/ERK signaling axis: in-silico and in vitro studies.Naunyn-Schmiedeberg's archives of pharmacology · 2024Article
- SPRank─A Knowledge-Based Scoring Function for RNA-Ligand Pose Prediction and Virtual Screening.Journal of chemical theory and computation · 2024Article
- Advances in machine-learning approaches to RNA-targeted drug design.Artificial intelligence chemistry · 2024Article
- Review
- HIV-1 Transcription Inhibition Using Small RNA-Binding Molecules.Pharmaceuticals (Basel, Switzerland) · 2023Article
- Comparative Assessment of Docking Programs for Docking and Virtual Screening of Ribosomal Oxazolidinone Antibacterial Agents.Antibiotics (Basel, Switzerland) · 2023Article
- Virtual Screening-Based Drug Development for the Treatment of Nervous System Diseases.Current neuropharmacology · 2023Review
- Role and Perspective of Molecular Simulation-Based Investigation of RNA-Ligand Interaction: From Small Molecules and Peptides to Photoswitchable RNA Binding.Molecules (Basel, Switzerland) · 2021Review
- RNA-ligand molecular docking: advances and challenges.Wiley interdisciplinary reviews. Computational molecular scienceArticle
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
In this review, we retraced the '40-year evolution' of molecular docking algorithms. Over the course of the years, their development allowed to progress from the so-called 'rigid-docking' searching methods to the more sophisticated 'semi-flexible' and 'flexible docking' algorithms. Together with the advancement of computing architecture and power, molecular docking's applications also exponentially increased, from a single-ligand binding calculation to large screening and polypharmacology profiles. Recently targeting nucleic acids with small molecules has emerged as a valuable therapeutic strategy especially for cancer treatment, along with bacterial and viral infections. For example, therapeutic intervention at the mRNA level allows to overcome the problematic of undruggable proteins without modifying the genome. Despite the promising therapeutic potential of nucleic acids, molecular docking programs have been optimized mostly for proteins. Here, we have analyzed literature data on nucleic acid to benchmark some of the widely used docking programs. Finally, the comparison between proteins and nucleic acid targets docking highlighted similarity and differences, which are intrinsically related to their chemical and structural nature.
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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.