SMARTFlexDB 发布配对 apo–holo RNA 结构数据库与分析平台
SMARTFlexDB: a paired apo–holo RNA structure database and analysis platform for RNA conformational flexibility and small-molecule recognition
SMARTFlexDB 是一个整理并分析配对 apo–holo RNA 结构的数据库与分析平台，用于刻画 RNA 结合小分子前后的构象差异和 RNA–小分子识别。研究者在 PDB 中按 RNA 链序列一致性与覆盖度至少 90%、结合口袋核苷酸完全保守的标准筛选配对。当前版本包含 266 个 holo 结构中的 434 个结合口袋，与 186 个 apo 结构关联，得到 1187 个口袋层面的 apo–holo 配对，整理为 734 条数据库条目，覆盖 150 种小分子和 23 个 RNA 功能类别。
来源：Nucleic Acids Research · doi.org
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/.