ArticleBioinformatics (Oxford, England)2026
RAFA: RNA all-atom structure reconstruction from sparse anchor coordinates.
Article in Bioinformatics (Oxford, England), 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
summaryWe 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. AVAILABILITY AND IMPLEMENTATION: RAFA is available at https://github.com/wangleiofficial/RAFA and archived at https://doi.org/10.5281/zenodo.20951205.
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