lociPARSE: A Locality-aware Invariant Point Attention Model for Scoring RNA 3D Structures

J Chem Inf Model. 2024 Nov 25;64(22):8655-8664. doi: 10.1021/acs.jcim.4c01621. Epub 2024 Nov 11.

Abstract

A scoring function that can reliably assess the accuracy of a 3D RNA structural model in the absence of experimental structure is not only important for model evaluation and selection but also useful for scoring-guided conformational sampling. However, high-fidelity RNA scoring has proven to be difficult using conventional knowledge-based statistical potentials and currently available machine learning-based approaches. Here, we present lociPARSE, a locality-aware invariant point attention architecture for scoring RNA 3D structures. Unlike existing machine learning methods that estimate superposition-based root-mean-square deviation (RMSD), lociPARSE estimates Local Distance Difference Test (lDDT) scores capturing the accuracy of each nucleotide and its surrounding local atomic environment in a superposition-free manner, before aggregating information to predict global structural accuracy. Tested on multiple datasets including CASP15, lociPARSE significantly outperforms existing statistical potentials (rsRNASP, cgRNASP, DFIRE-RNA, and RASP) and machine learning methods (ARES and RNA3DCNN) across complementary assessment metrics. lociPARSE is freely available at https://github.com/Bhattacharya-Lab/lociPARSE.

MeSH terms

  • Machine Learning
  • Models, Molecular*
  • Nucleic Acid Conformation*
  • RNA* / chemistry
  • Software

Substances

  • RNA