PARSEbp: pairwise agreement-based RNA scoring with emphasis on base pairings.

Motivation: High-fidelity scoring of RNA three-dimensional structures remains a major challenge in RNA structure prediction and conformational sampling. While single-model methods for scoring RNA structures can capture individual structural features, they fail to capture the broader structural consensus within a conformational ensemble, limiting their effectiveness in ranking and model selection. Results: We present PARSEbp, a fast and effective multi-model RNA scoring method that integrates pairwise structural agreement across the conformational ensemble with base pairing consistency. By leveraging both alignment-based global structural agreement at the three-dimensional level and base pairing consistency at the two-dimensional level, PARSEbp efficiently constructs a consensus similarity matrix from which per-structure accuracy scores are computed. Tested on RNA targets from the Critical Assessment of Structure Prediction (CASP) challenges CASP16 and CASP15, PARSEbp significantly outperforms existing single- and multi-model RNA scoring functions, including traditional statistical potentials, state-of-the-art deep learning methods, and consensus-based approaches, as well as a baseline variant of PARSEbp without the emphasis on base pairings, across a wide range of complementary assessment metrics. Availability and implementation: PARSEbp is freely available at https://github.com/Bhattacharya-Lab/PARSEbp.