tooluniverse-binder-discovery

name	tooluniverse-binder-discovery
description	Discover novel small-molecule binders for protein targets using structure-based and ligand-based screening. Covers druggability assessment, known-ligand mining (ChEMBL, BindingDB), similarity expansion, ADMET filtering, and synthesis feasibility. Use for hit identification, virtual screening, target-to-compounds workflows, and lead-finding before commit-to-medchem.

Small Molecule Binder Discovery Strategy

Systematic discovery of novel small molecule binders using 60+ ToolUniverse tools across druggability assessment, known ligand mining, similarity expansion, ADMET filtering, and synthesis feasibility.

LOOK UP DON'T GUESS - Always retrieve actual data from tools before drawing conclusions. Do not assume druggability, binding sites, or compound properties based on target class alone.

KEY PRINCIPLES:

1. Report-first approach - Create report file FIRST, then populate progressively
2. Target validation FIRST - Confirm druggability before compound searching
3. Multi-strategy approach - Combine structure-based and ligand-based methods
4. ADMET-aware filtering - Eliminate poor compounds early
5. Evidence grading - Grade candidates by supporting evidence
6. Actionable output - Provide prioritized candidates with rationale
7. English-first queries - Always use English terms in tool calls. Respond in the user's language

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Binding Site Reasoning (Start Here)

Before any tool call, reason about the target's structural biology:

Is the binding site a well-defined pocket (small molecule accessible) or a flat protein-protein interface (needs peptide/macrocycle)? This determines your screening strategy.

• Enzymes with active sites (proteases, kinases, ATPases): deep, well-defined pockets. Classic small molecule territory. Prioritize co-crystal structure search and known inhibitor scaffold analysis.