RAFA: RNA all-atom structure reconstruction from sparse anchor coordinates.

Authors

Lei Wang, Zilu Zeng

Published in

Bioinformatics (Oxford, England). Oct 06, 2026. Epub Oct 06, 2026.

Abstract

We present RAFA, a C ++ command-line tool for RNA all-atom structure reconstruction from sparse or partial coordinates. RAFA targets settings in which coarse-grained modelling, low-resolution fitting, or partial experimental interpretation provides RNA anchor atoms but not a complete atomic model. The method retrieves experimentally observed 3-5 nt all-atom RNA fragments, fits them to local anchors, combines overlapping fragment-derived coordinate estimates by weighted consensus, and routes sparse and rich inputs through distinct reconstruction paths. In an independent RNA3DB train/test evaluation, no library-test pair exceeded 80% global sequence identity. RAFA achieved lower all-atom root-mean-square deviation (RMSD) values than Arena in 73.3% of target-mode comparisons, with the largest gains in input modes with the fewest structural constraints.
RAFA is available at https://github.com/wangleiofficial/RAFA and archived at https://doi.org/10.5281/zenodo.20951205.
Supplementary data are available at Bioinformatics online.

PMID:
42836828
Bibliographic data and abstract were imported from PubMed on 06 Oct 2026.

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