LIGAND DATA

This section presents the ligand data available in HARIBOSS, with a particular focus on ligand selectivity toward their RNA targets. For each RNA family, the number of associated ligands is reported and categorized into specific binders, which are observed in a single RNA family, and shared binders, which are found across multiple families. The same specificity analysis is also provided for different molecular environments. An interactive TMAP complements these statistics by mapping the chemical space of all ligands, colored by RNA family, enabling the exploration of chemically related compounds as well as family-specific chemical clusters.

Interactive TMAP by RNA family

Tip: click inside the TMAP, then use Ctrl + mouse wheel to zoom and pan.

Open TMAP in full page viewer

Searching by SMILES

You can search for compounds using their Canonical SMILES notation directly from the compounds page search bar. The search performs a case-insensitive substring match on the SMILES strings.

Tip: You can search using complete SMILES strings or partial patterns.

Examples:

CCO - Find ethanol and compounds containing this pattern
c1ccccc1 - Find benzene and aromatic compounds
CC(=O)O - Find carboxylic acid derivatives

SMILES notation basics:

Atoms are represented by their chemical symbols (C, N, O, etc.)
Lowercase letters indicate aromatic atoms (c, n, o)
Numbers indicate ring closures (c1ccccc1 = benzene ring)
Bonds: = (double), # (triple), single bonds are implicit
Parentheses () indicate branching

Learn more about SMILES notation

Searching by SMARTS

You can also search for compounds using their SMARTS (SMiles ARbitrary Target Specification) notation directly from the compounds page search bar. The search performs a case-insensitive substring match on the SMARTS strings.

Tip: SMARTS allows more expressive pattern matching than SMILES, including generic atoms and bonds.

Examples:

[CH3][CH2][OH] - Find ethanol and compounds containing this pattern
[c]1[c][c][c][c][c]1 - Find aromatic rings
[#6]=[#8] - Find carbonyl groups (C=O)

SMARTS notation basics:

Atoms are represented by their chemical symbols, optionally with hydrogens (e.g., [CH3])
* or [*] matches any atom
#6 matches any carbon, #7 any nitrogen, etc.
Bond symbols: - (single), = (double), # (triple), : (aromatic)
Recursive SMARTS can describe more complex substructures

Learn more about SMARTS notation