RAFA: RNA all-atom structure reconstruction from sparse anchor coordinates.
- 1State Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, China.
- 2School of Software Engineering, Huazhong University of Science and Technology, Wuhan 430074, China.
- 3Wuhan Children's Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430070, China.
Abstract
Summary
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.Availability and implementation
RAFA is available at https://github.com/wangleiofficial/RAFA and archived at https://doi.org/10.5281/zenodo.20951205.
Related
- HLA class I anchor motifs contribute to antigen presentation from non-canonical open reading frames
- The BAF chromatin remodeling subunit ARID1B coordinates cell-cycle exit and motor neuron differentiation
- Substrate-induced asymmetry coordinates lipoprotein handover and abaucin trapping in Acinetobacter baumannii LolDF
- ORMDL3-mediated SPT regulation Coordinates Myelin Sphingolipid and Protein Synthesis in Oligodendrocytes
- Firrm functions as a multiprotein interaction platform that coordinates Mcm8-9-Hrob recruitment and Fignl1-mediated Rad51 unloading
BibTeX
@article{wang2026rafa,
title = {{RAFA: RNA all-atom structure reconstruction from sparse anchor coordinates.}},
author = {Lei Wang and Zilu Zeng},
journal = {Bioinformatics (Oxford, England)},
year = {2026},
month = oct,
doi = {10.1093/bioinformatics/btag746},
url = {https://europepmc.org/article/MED/42836828},
note = {CC BY},
}
RIS
TY - JOUR
TI - RAFA: RNA all-atom structure reconstruction from sparse anchor coordinates.
AU - Lei Wang
AU - Zilu Zeng
PY - 2026
DA - 2026/10/01
JO - Bioinformatics (Oxford, England)
DO - 10.1093/bioinformatics/btag746
UR - https://europepmc.org/article/MED/42836828
AB - Summary 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.Availability and implementation RAFA is available at https://github.com/wangleiofficial/RAFA and archived at https://doi.org/10.5281/zenodo.20951205.
SN - 1367-4803
SN - 1367-4811
ER -