ArticleNucleic acids research2017
SPA-LN: a scoring function of ligand-nucleic acid interactions via optimizing both specificity and affinity.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 43 citations in OpenAlex.
- Machine Learning for RNA-Targeting Drug Design.Journal of chemical information and modeling · 2026Review
- Comparative Evaluation of Explicit Solvent Models for RNA-Ligand Docking.Journal of chemical information and modeling · 2026Article
- Binding Specificity and Local Frustration in Structure-based Drug Discovery.Current medicinal chemistry · 2026Review
- RLDOCKScore: A Scoring Function for RNA-Ligand Docking and Small Molecule Virtual Screening.Journal of chemical theory and computation · 2025Article
- Harnessing Computational Approaches for RNA-Targeted Drug Discovery.RNA nanomed · 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
- Contrastive pre-training and 3D convolution neural network for RNA and small molecule binding affinity prediction.Bioinformatics (Oxford, England) · 2024Article
- RmsdXNA: RMSD prediction of nucleic acid-ligand docking poses using machine-learning method.Briefings in bioinformatics · 2024Article
- Comparative Assessment of Docking Programs for Docking and Virtual Screening of Ribosomal Oxazolidinone Antibacterial Agents.Antibiotics (Basel, Switzerland) · 2023Article
- Design and Prediction of Aptamers Assisted by In Silico Methods.Biomedicines · 2023Review
- Electrochemical Aptasensors for Antibiotics Detection: Recent Achievements and Applications for Monitoring Food Safety.Sensors (Basel, Switzerland) · 2022Review
- Perspectives on the landscape and flux theory for describing emergent behaviors of the biological systems.Journal of biological physics · 2022Review
- RNALigands: a database and web server for RNA-ligand interactions.RNA (New York, N.Y.) · 2022Article
- AnnapuRNA: A scoring function for predicting RNA-small molecule binding poses.PLoS computational biology · 2021Article
- Methods and Applications of In Silico Aptamer Design and Modeling.International journal of molecular sciences · 2020Review
- Augmented base pairing networks encode RNA-small molecule binding preferences.Nucleic acids research · 2020Article
- How 'Protein-Docking' Translates into the New Emerging Field of Docking Small Molecules to Nucleic Acids?Molecules (Basel, Switzerland) · 2020Review
- Benchmarking of different molecular docking methods for protein-peptide docking.BMC bioinformatics · 2019Article
- Site-selective photoinduced cleavage and profiling of DNA by chiral semiconductor nanoparticles.Nature chemistry · 2018Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Nucleic acids have been widely recognized as potential targets in drug discovery and aptamer selection. Quantifying the interactions between small molecules and nucleic acids is critical to discover lead compounds and design novel aptamers. Scoring function is normally employed to quantify the interactions in structure-based virtual screening. However, the predictive power of nucleic acid-ligand scoring functions is still a challenge compared to other types of biomolecular recognition. With the rapid growth of experimentally determined nucleic acid-ligand complex structures, in this work, we develop a knowledge-based scoring function of nucleic acid-ligand interactions, namely SPA-LN. SPA-LN is optimized by maximizing both the affinity and specificity of native complex structures. The development strategy is different from those of previous nucleic acid-ligand scoring functions which focus on the affinity only in the optimization. The native conformation is stabilized while non-native conformations are destabilized by our optimization, making the funnel-like binding energy landscape more biased toward the native state. The performance of SPA-LN validates the development strategy and provides a relatively more accurate way to score the nucleic acid-ligand interactions.
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