ArticleBiophysical journal2022
rsRNASP: A residue-separation-based statistical potential for RNA 3D structure evaluation.
Article in Biophysical journal, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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26 citing papers in PubMed.
- Spectral Graph Features for Reference-free RNA 3D Quality Assessment.bioRxiv : the preprint server for biology · 2026Article
- R3J-AGNN: GNN-Based Prediction of Inter-Branch Angles in RNA Three-Way Junctions from Secondary Structure.Biology · 2026Article
- Computational approaches for RNA structure prediction and design.Cell reports. Physical science · 2026Article
- gCoSRNA: Generalizable Coaxial Stacking Prediction for RNA Junctions Using Secondary Structure.Biomolecules · 2026Article
- Integrated experimental and AI innovations for RNA structure determination.Nature biotechnology · 2026Review
- Quality assessment of RNA 3D structure models using deep learning and intermediate 2D maps.Communications biology · 2026Article
- TiRNA: a coarse-grained method with temperature and ion effects for RNA structure folding and prediction.Nucleic acids research · 2026Article
- PARSEbp: pairwise agreement-based RNA scoring with emphasis on base pairings.Bioinformatics advances · 2026Article
- RNAdvisor 2: A unified platform for RNA 3D model quality assessment using metrics, scoring functions, and meta-metrics.Scientific reports · 2025Article
- RNAtive to recognize native-like structure in a set of RNA 3D models.Bioinformatics (Oxford, England) · 2025Article
- PARSEbp: Pairwise Agreement-based RNA Scoring with Emphasis on Base Pairings.bioRxiv : the preprint server for biology · 2025Article
- rsRNASP1: A distance- and dihedral-dependent statistical potential for RNA 3D structure evaluation.Biophysical journal · 2025Article
- 3D structure and stability prediction of DNA with multi-way junctions in ionic solutions.PLoS computational biology · 2025Article
- RNA-TorsionBERT: leveraging language models for RNA 3D torsion angles prediction.Bioinformatics (Oxford, England) · 2024Article
- lociPARSE: A Locality-aware Invariant Point Attention Model for Scoring RNA 3D Structures.Journal of chemical information and modeling · 2024Article
- IsRNAcirc: 3D structure prediction of circular RNAs based on coarse-grained molecular dynamics simulation.PLoS computational biology · 2024Article
- 3dDNAscoreA: A scoring function for evaluation of DNA 3D structures.Biophysical journal · 2024Article
- lociPARSE: a locality-aware invariant point attention model for scoring RNA 3D structures.bioRxiv : the preprint server for biology · 2024Article
- RNAdvisor: a comprehensive benchmarking tool for the measure and prediction of RNA structural model quality.Briefings in bioinformatics · 2024Article
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Abstract
Knowledge-based statistical potentials have been shown to be rather effective in protein 3-dimensional (3D) structure evaluation and prediction. Recently, several statistical potentials have been developed for RNA 3D structure evaluation, while their performances are either still at a low level for the test datasets from structure prediction models or dependent on the "black-box" process through neural networks. In this work, we have developed an all-atom distance-dependent statistical potential based on residue separation for RNA 3D structure evaluation, namely rsRNASP, which is composed of short- and long-ranged potentials distinguished by residue separation. The extensive examinations against available RNA test datasets show that rsRNASP has apparently higher performance than the existing statistical potentials for the realistic test datasets with large RNAs from structure prediction models, including the newly released RNA-Puzzles dataset, and is comparable to the existing top statistical potentials for the test datasets with small RNAs or near-native decoys. In addition, rsRNASP is superior to RNA3DCNN, a recently developed scoring function through 3D convolutional neural networks. rsRNASP and the relevant databases are available to the public.
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