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Peer-reviewedCC BY-NC 4.0Nucleic Acids Research

SMARTFlexDB: a paired apo–holo RNA structure database and analysis platform for RNA conformational flexibility and small-molecule recognition

  • Shiyu Jiang1,2
  • Jinhang Wei1,2
  • Amirhossein Taghavi3
  • Gustavo Seabra1
  • Jessica L Childs-Disney3
  • Chenglong Li1
  • Matthew D Disney3,4
  • Yanjun Li1,2
4 affiliations
  1. 1Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida , Gainesville, FL 32610 ,
  2. 2Department of Computer & Information Science & Engineering, University of Florida , Gainesville, FL 32611 ,
  3. 3Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology , 130 Scripps Way, Jupiter, FL 33458 ,
  4. 4Department of Chemistry, The Scripps Research Institute , 130 Scripps Way, Jupiter, FL 33458 ,
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Abstract

RNA structures can undergo substantial conformational changes upon small-molecule binding, yet existing structural resources provide only static RNA–ligand snapshots without connecting ligand-bound (holo) RNA structures to corresponding ligand-free (apo) conformations. SMARTFlexDB is a curated database and analysis platform that uses paired apo–holo RNA structures to characterize conformational differences and RNA–small molecule recognition. Candidate pairs were identified from the Protein Data Bank by matching RNA chains with at least 90% sequence identity and coverage, and fully conserved binding pocket nucleotides. The current release contains 434 binding pockets from 266 holo structures, linked to 186 apo structures to yield 1187 pocket-level apo–holo pairs organized into 734 database entries, spanning 150 small molecules and 23 RNA functional classes. Each entry integrates RNA sequence and secondary-structure annotations, apo and holo three-dimensional structures, RNA–ligand atomic interactions, and quantitative descriptors of global and local conformational changes. An interactive web interface enables users to explore sequence alignments and structural overlays, compare secondary structures and RNA motifs, and upload paired apo–holo structures for customized analysis. By linking ligand-bound and ligand-free RNA structures, SMARTFlexDB provides a robust foundation for investigating RNA structural flexibility and supporting RNA-targeted small-molecule drug discovery. The database and analysis platform are available at https://aidd.rc.ufl.edu/app/smartflexdb/.

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Cite

BibTeXRIS
BibTeX
@article{jiang2026smartflexdb,
  title = {{SMARTFlexDB: a paired apo–holo RNA structure database and analysis platform for RNA conformational flexibility and small-molecule recognition}},
  author = {Shiyu Jiang and Jinhang Wei and Amirhossein Taghavi and Gustavo Seabra and Jessica L Childs-Disney and Chenglong Li and Matthew D Disney and Yanjun Li},
  journal = {Nucleic Acids Research},
  year = {2026},
  month = oct,
  doi = {10.1093/nar/gkag1029},
  url = {https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkag1029/9001949},
  note = {CC BY-NC 4.0},
}
RIS
TY  - JOUR
TI  - SMARTFlexDB: a paired apo–holo RNA structure database and analysis platform for RNA conformational flexibility and small-molecule recognition
AU  - Shiyu Jiang
AU  - Jinhang Wei
AU  - Amirhossein Taghavi
AU  - Gustavo Seabra
AU  - Jessica L Childs-Disney
AU  - Chenglong Li
AU  - Matthew D Disney
AU  - Yanjun Li
PY  - 2026
DA  - 2026/10/26
JO  - Nucleic Acids Research
DO  - 10.1093/nar/gkag1029
UR  - https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkag1029/9001949
AB  - RNA structures can undergo substantial conformational changes upon small-molecule binding, yet existing structural resources provide only static RNA–ligand snapshots without connecting ligand-bound (holo) RNA structures to corresponding ligand-free (apo) conformations. SMARTFlexDB is a curated database and analysis platform that uses paired apo–holo RNA structures to characterize conformational differences and RNA–small molecule recognition. Candidate pairs were identified from the Protein Data Bank by matching RNA chains with at least 90% sequence identity and coverage, and fully conserved binding pocket nucleotides. The current release contains 434 binding pockets from 266 holo structures, linked to 186 apo structures to yield 1187 pocket-level apo–holo pairs organized into 734 database entries, spanning 150 small molecules and 23 RNA functional classes. Each entry integrates RNA sequence and secondary-structure annotations, apo and holo three-dimensional structures, RNA–ligand atomic interactions, and quantitative descriptors of global and local conformational changes. An interactive web interface enables users to explore sequence alignments and structural overlays, compare secondary structures and RNA motifs, and upload paired apo–holo structures for customized analysis. By linking ligand-bound and ligand-free RNA structures, SMARTFlexDB provides a robust foundation for investigating RNA structural flexibility and supporting RNA-targeted small-molecule drug discovery. The database and analysis platform are available at https://aidd.rc.ufl.edu/app/smartflexdb/.
SN  - 0305-1048
SN  - 1362-4962
ER  -