RNA STRAND v2.0 - The RNA secondary STRucture and statistical ANalysis Database

Search Criteria (click here to expand/contract) General features Type: Any Organism: Any Source: Any , Source ID: Any Length: Any Validated by NMR or X-Ray: I don't care Number of molecules in complex: Any Fragment: I don't care Duplicates: All molecules Sequence pattern: Any Abstract shape: Any Pseudoknot features Number of pseudoknots per molecule: Greater than or equal to 1

Search results: 2333 results found. (Click on the row to see the statistics for the chosen molecule.) RNA STRAND ID [?] Molecule name [?] Type [?] Organism [?] Source [?] Source ID [?] Length [?] PDB_00123 HIV-1(MAL) RNA DIMERIZATION INITIATION SITE Synthetic RNA SYNTHETIC RCSB Protein Data Bank 1K9W 92 PDB_00124 CONFORMATION OF AN RNA PSEUDOKNOT FROM MOUSE MAMMARY TUMOR VIRUS, NMR, 1 STRUCTURE Synthetic RNA SYNTHETIC RCSB Protein Data Bank 1KAJ 32 PDB_00128 TAR-TAR "KISSING" HAIRPIN COMPLEX DERIVED FROM THE HIV GENOME, NMR, 1 STRUCTURE Synthetic RNA SYNTHETIC RCSB Protein Data Bank 1KIS 32 PDB_00133 A MUTANT RNA PSEUDOKNOT THAT PROMOTES RIBOSOMAL FRAMESHIFTING IN MOUSE MAMMARY TUMOR VIRUS, NMR, MIN Other rRNA Unknown RCSB Protein Data Bank 1KPD 32 PDB_00134 PEMV-1 P1-P2 FRAMESHIFTING PSEUDOKNOT, 15 LOWEST ENERGY STRUCTURES Synthetic RNA SYNTHETIC RCSB Protein Data Bank 1KPY 28 PDB_00135 PEMV-1 P1-P2 FRAMESHIFTING PSEUDOKNOT REGULARIZED AVERAGE STRUCTURE Synthetic RNA SYNTHETIC RCSB Protein Data Bank 1KPZ 28 PDB_00138 ATOMIC RESOLUTION CRYSTAL STRUCTURE OF A VIRAL RNA PSEUDOKNOT Viral & Phage Unknown RCSB Protein Data Bank 1L2X 28 PDB_00139 LOW RESOLUTION CRYSTAL STRUCTURE OF A VIRAL RNA PSEUDOKNOT Viral & Phage Unknown RCSB Protein Data Bank 1L3D 28 PDB_00140 CRYSTAL STRUCTURE OF A MUTANT (C109G,G212C) P4-P6 DOMAIN OF THE GROUP I INTRON FROM TETRAHYMENA THER GI Intron Unknown RCSB Protein Data Bank 1L8V 314 PDB_00187 THE CRYSTAL STRUCTURE OF THE 50S LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS COMPLEXED WITH 23S rRNA DEINOCOCCUS RADIODURANS RCSB Protein Data Bank 1P9X 2738

Analyse the 2333 results of your search Per molecule: Molecule length Number of stems Number of hairpin loops Number of bulges Number of internal loops Number of multi-loops Number of pseudoknots Number of bands Number of domains # base pairs to break for pseudoknot freeness # bands to break for pseudoknot freeness Average stem length Average hairpin size Average bulge size Average internal loop size Average multi-loop size Cumulative distribution Histograms Correlation vs. molecule length In all 2333 molecules: Stem length Stem free energy (estimated) Hairpin number of free bases Bulge number of free bases Internal loop number of free bases Internal loop absolute asymmetry Multi-loop number of free bases Multi-loop average absolute asymmetry Multi-loop number of branches Exterior loop number of free bases Pseudoknot number of bands Pseudoknot - min # of base pairs to break Pseudoknot - min # of bands to break Pseudoknot length Number of non-canonical base pairs and nearest neighbours Cumulative distribution Histograms (Cummulative distributions are not applicable to non-canonical base pairs) Remove outliers (not applicable to correlations and non-canonical base pairs) [?] Normalize by RNA type (not applicable to non-canonical base pairs) [?]

Download all 2333 results of your search Format [?]: CT (one file per entry) RNAML (one file per entry) BPSEQ (one file per entry) Dot-parentheses (one file per entry) Dot-parentheses (one file for all entries) FASTA (one file per entry) FASTA (one file for all entries)