@bgicli/bgicli 2.1.1 → 2.2.0

package/data/skills/tooluniverse-binder-discovery/SKILL.md

@@ -0,0 +1,1459 @@
+---
+name: tooluniverse-binder-discovery
+description: Discover novel small molecule binders for protein targets using structure-based and ligand-based approaches. Creates actionable reports with candidate compounds, ADMET profiles, and synthesis feasibility. Use when users ask to find small molecules for a target, identify novel binders, perform virtual screening, or need hit-to-lead compound identification.
+---
+
+# 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.
+
+**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, even if the user writes in another language. Only try original-language terms as a fallback. Respond in the user's language
+
+---
+
+## Critical Workflow Requirements
+
+### 1. Report-First Approach (MANDATORY)
+
+**DO NOT** show search process or tool outputs to the user. Instead:
+
+1. **Create the report file FIRST** - Before any data collection:
+   - File name: `[TARGET]_binder_discovery_report.md`
+   - Initialize with all section headers from the template
+   - Add placeholder text: `[Researching...]` in each section
+
+2. **Progressively update the report** - As you gather data:
+   - Update each section with findings immediately
+   - The user sees the report growing, not the search process
+
+3. **Output separate data files**:
+   - `[TARGET]_candidate_compounds.csv` - Prioritized compounds with SMILES, scores
+   - `[TARGET]_bibliography.json` - Literature references (optional)
+
+### 2. Citation Requirements (MANDATORY)
+
+Every piece of information MUST include its source:
+
+```markdown
+### 3.2 Known Inhibitors
+| Compound | ChEMBL ID | IC50 (nM) | Selectivity | Source |
+|----------|-----------|-----------|-------------|--------|
+| Imatinib | CHEMBL941 | 38 | ABL-selective | ChEMBL |
+| Dasatinib | CHEMBL1421 | 0.5 | Multi-kinase | ChEMBL |
+
+*Source: ChEMBL via `ChEMBL_get_target_activities` (CHEMBL1862)*
+```
+
+---
+
+## Workflow Overview
+
+```
+Phase 0: Tool Verification (check parameter names)
+    ↓
+Phase 1: Target Validation
+    ├─ 1.1 Resolve identifiers (UniProt, Ensembl, ChEMBL target ID)
+    ├─ 1.2 Assess druggability/tractability
+    │   └─ 1.2.5 Check therapeutic antibodies (Thera-SAbDab) [NEW]
+    ├─ 1.3 Identify binding sites
+    └─ 1.4 Predict structure (NvidiaNIM_alphafold2/esmfold)
+    ↓
+Phase 2: Known Ligand Mining
+    ├─ Extract ChEMBL bioactivity data
+    ├─ Get GtoPdb interactions
+    ├─ Identify chemical probes
+    ├─ BindingDB affinity data (NEW - Ki/IC50/Kd)
+    ├─ PubChem BioAssay HTS data (NEW - screening hits)
+    └─ Analyze SAR from known actives
+    ↓
+Phase 3: Structure Analysis
+    ├─ Get PDB structures with ligands
+    ├─ Check EMDB for cryo-EM structures (NEW - for membrane targets)
+    ├─ Analyze binding pocket
+    └─ Identify key interactions
+    ↓
+Phase 3.5: Docking Validation (NvidiaNIM_diffdock/boltz2) [NEW]
+    ├─ Dock reference inhibitor
+    └─ Validate binding pocket geometry
+    ↓
+Phase 4: Compound Expansion
+    ├─ 4.1-4.3 Similarity/substructure search
+    └─ 4.4 De novo generation (NvidiaNIM_genmol/molmim) [NEW]
+    ↓
+Phase 5: ADMET Filtering
+    ├─ Predict physicochemical properties
+    ├─ Predict ADMET endpoints
+    └─ Flag liabilities
+    ↓
+Phase 6: Candidate Docking & Prioritization
+    ├─ Dock all candidates (NvidiaNIM_diffdock/boltz2) [UPDATED]
+    ├─ Score by docking + ADMET + novelty
+    ├─ Assess synthesis feasibility
+    └─ Generate final ranked list
+    ↓
+Phase 7: Report Synthesis
+```
+
+---
+
+## Phase 0: Tool Verification
+
+**CRITICAL**: Verify tool parameters before calling unfamiliar tools.
+
+```python
+# Check tool params to prevent silent failures
+tool_info = tu.tools.get_tool_info(tool_name="ChEMBL_get_target_activities")
+```
+
+### Known Parameter Corrections
+
+| Tool | WRONG Parameter | CORRECT Parameter |
+|------|-----------------|-------------------|
+| `OpenTargets_get_target_tractability_by_ensemblID` | `ensembl_id` | `ensemblId` |
+| `ChEMBL_get_target_activities` | `chembl_target_id` | `target_chembl_id` |
+| `ChEMBL_search_similar_molecules` | `smiles` | `molecule` (accepts SMILES, ChEMBL ID, or name) |
+| `alphafold_get_prediction` | `uniprot` | `accession` |
+
+---
+
+## Phase 1: Target Validation
+
+### 1.1 Identifier Resolution Chain
+
+```
+1. UniProt_search(query=target_name, organism="human")
+   └─ Extract: UniProt accession, gene name, protein name
+
+2. MyGene_query_genes(q=gene_symbol, species="human")
+   └─ Extract: Ensembl gene ID, NCBI gene ID
+
+3. ChEMBL_search_targets(query=target_name, organism="Homo sapiens")
+   └─ Extract: ChEMBL target ID, target type
+
+4. GtoPdb_get_targets(query=target_name)
+   └─ Extract: GtoPdb target ID (if GPCR/ion channel/enzyme)
+```
+
+**Store all IDs for downstream queries**:
+```
+ids = {
+    'uniprot': 'P00533',
+    'ensembl': 'ENSG00000146648',
+    'chembl_target': 'CHEMBL203',
+    'gene_symbol': 'EGFR',
+    'gtopdb': '1797'  # if available
+}
+```
+
+### 1.2 Druggability Assessment
+
+**Multi-Source Triangulation**:
+
+```
+1. OpenTargets_get_target_tractability_by_ensemblID(ensemblId)
+   └─ Extract: Small molecule tractability score, bucket
+   
+2. DGIdb_get_gene_druggability(genes=[gene_symbol])
+   └─ Extract: Druggability categories, known drug count
+   
+3. OpenTargets_get_target_classes_by_ensemblID(ensemblId)
+   └─ Extract: Target class (kinase, GPCR, etc.)
+
+4. GPCRdb_get_protein(protein=entry_name)  # NEW - for GPCRs
+   └─ Extract: GPCR family, receptor state, ligand binding data
+```
+
+### 1.2a GPCRdb Integration (NEW - for GPCR Targets)
+
+~35% of all approved drugs target GPCRs. For GPCR targets, use specialized data:
+
+```python
+def check_if_gpcr_and_enrich(tu, target_name, uniprot_id):
+    """Check if target is GPCR and get specialized data."""
+    
+    # Build GPCRdb entry name (e.g., "adrb2_human")
+    entry_name = f"{target_name.lower()}_human"
+    
+    # Check if it's a GPCR
+    gpcr_info = tu.tools.GPCRdb_get_protein(
+        operation="get_protein",
+        protein=entry_name
+    )
+    
+    if gpcr_info.get('status') == 'success':
+        # It's a GPCR - get specialized data
+        
+        # Get known structures (active/inactive states)
+        structures = tu.tools.GPCRdb_get_structures(
+            operation="get_structures",
+            protein=entry_name
+        )
+        
+        # Get known ligands
+        ligands = tu.tools.GPCRdb_get_ligands(
+            operation="get_ligands",
+            protein=entry_name
+        )
+        
+        # Get mutation data (important for SAR)
+        mutations = tu.tools.GPCRdb_get_mutations(
+            operation="get_mutations",
+            protein=entry_name
+        )
+        
+        return {
+            'is_gpcr': True,
+            'gpcr_family': gpcr_info['data'].get('family'),
+            'gpcr_class': gpcr_info['data'].get('receptor_class'),
+            'structures': structures['data'].get('structures', []),
+            'ligands': ligands['data'].get('ligands', []),
+            'mutation_data': mutations['data'].get('mutations', [])
+        }
+    
+    return {'is_gpcr': False}
+```
+
+**GPCRdb Advantages**:
+- GPCR-specific sequence alignments (Ballesteros-Weinstein numbering)
+- Active vs. inactive state structures
+- Curated ligand binding data
+- Experimental mutation effects on ligand binding
+
+**Druggability Scorecard**:
+
+| Factor | Assessment | Score |
+|--------|------------|-------|
+| Known small molecule drugs | Yes (3+) | ★★★ |
+| Tractability bucket | 1-3 | ★★☆-★★★ |
+| Target class | Enzyme/GPCR/Ion channel | ★★★ |
+| Binding site known | Yes (X-ray) | ★★★ |
+| GPCRdb ligands available | Yes (10+) | ★★★ (GPCR only) |
+| Therapeutic antibodies exist | Check Thera-SAbDab | See 1.2.5 |
+
+**Decision Point**: If druggability score < ★★☆, warn user about challenges.
+
+### 1.2.5 Therapeutic Antibody Landscape (NEW)
+
+Check if therapeutic antibodies already target this protein - important for:
+- Understanding competitive landscape
+- Validating target tractability (if antibodies work, target is validated)
+- Identifying potential combination approaches
+
+```python
+def check_therapeutic_antibodies(tu, target_name):
+    """
+    Check Thera-SAbDab for therapeutic antibodies against target.
+    """
+    # Search by target name
+    results = tu.tools.TheraSAbDab_search_by_target(
+        target=target_name
+    )
+    
+    if results.get('status') == 'success':
+        antibodies = results['data'].get('therapeutics', [])
+        
+        # Categorize by clinical stage
+        by_phase = {'Approved': [], 'Phase 3': [], 'Phase 2': [], 'Phase 1': [], 'Preclinical': []}
+        for ab in antibodies:
+            phase = ab.get('phase', 'Unknown')
+            for key in by_phase.keys():
+                if key.lower() in phase.lower():
+                    by_phase[key].append(ab)
+                    break
+        
+        return {
+            'total_antibodies': len(antibodies),
+            'by_phase': by_phase,
+            'antibodies': antibodies[:10],  # Top 10
+            'competitive_alert': len(by_phase.get('Approved', [])) > 0
+        }
+    return None
+
+def get_antibody_landscape(tu, target_name, uniprot_id=None):
+    """
+    Comprehensive antibody competitive landscape.
+    """
+    # Thera-SAbDab search
+    therasabdab = check_therapeutic_antibodies(tu, target_name)
+    
+    # Also search by common synonyms
+    synonyms = [target_name]
+    if target_name != uniprot_id:
+        synonyms.append(uniprot_id)
+    
+    all_antibodies = []
+    for synonym in synonyms:
+        results = tu.tools.TheraSAbDab_search_therapeutics(query=synonym)
+        if results.get('status') == 'success':
+            all_antibodies.extend(results['data'].get('therapeutics', []))
+    
+    # Deduplicate
+    seen = set()
+    unique = []
+    for ab in all_antibodies:
+        inn = ab.get('inn_name')
+        if inn and inn not in seen:
+            seen.add(inn)
+            unique.append(ab)
+    
+    return {
+        'antibodies': unique,
+        'count': len(unique),
+        'has_approved': any(ab.get('phase', '').lower() == 'approved' for ab in unique),
+        'source': 'Thera-SAbDab'
+    }
+```
+
+**Report Output**:
+```markdown
+### 1.2.5 Therapeutic Antibody Landscape (NEW)
+
+**Thera-SAbDab Search Results**:
+
+| Antibody (INN) | Target | Format | Phase | PDB |
+|----------------|--------|--------|-------|-----|
+| Pembrolizumab | PD-1 | IgG4 | Approved | 5DK3 |
+| Nivolumab | PD-1 | IgG4 | Approved | 5WT9 |
+| Cemiplimab | PD-1 | IgG4 | Approved | 7WVM |
+
+**Competitive Landscape**: ⚠️ 3 approved antibodies target this protein
+**Strategic Implication**: Small molecule approach offers differentiation (oral dosing, CNS penetration, cost)
+
+*Source: Thera-SAbDab via `TheraSAbDab_search_by_target`*
+```
+
+**Why Include Antibody Landscape**:
+- **Validation**: Approved antibodies = validated target
+- **Competition**: Understand what's already in market/clinic
+- **Strategy**: Identify gaps (no oral, no CNS-penetrant)
+- **Synergy**: Potential combination opportunities
+
+### 1.3 Binding Site Analysis
+
+```
+1. ChEMBL_search_binding_sites(target_chembl_id)
+   └─ Extract: Binding site names, types
+   
+2. get_binding_affinity_by_pdb_id(pdb_id)  # For each PDB with ligand
+   └─ Extract: Kd, Ki, IC50 values for co-crystallized ligands
+   
+3. InterPro_get_protein_domains(uniprot_accession)
+   └─ Extract: Domain architecture, active sites
+```
+
+**Output for Report**:
+```markdown
+### 1.3 Binding Site Assessment
+
+**Known Binding Sites**: 
+| Site | Type | Evidence | Key Residues | Source |
+|------|------|----------|--------------|--------|
+| ATP pocket | Orthosteric | X-ray (23 PDBs) | K745, E762, M793 | PDB/ChEMBL |
+| Allosteric pocket | Allosteric | X-ray (3 PDBs) | T790, C797 | PDB |
+
+**Binding Site Druggability**: ★★★ (well-defined pocket, multiple co-crystal structures)
+
+*Source: ChEMBL via `ChEMBL_search_binding_sites`, PDB structures*
+```
+
+### 1.4 Structure Prediction (NVIDIA NIM)
+
+When no experimental structure is available, or for custom domain predictions.
+
+**Requires**: `NVIDIA_API_KEY` environment variable
+
+**Option A: AlphaFold2 (High accuracy, async)**
+```
+NvidiaNIM_alphafold2(
+    sequence=kinase_domain_sequence,
+    algorithm="mmseqs2",
+    relax_prediction=False
+)
+└─ Returns: PDB structure with pLDDT confidence scores
+└─ Use when: Accuracy is critical, time is available (~5-15 min)
+```
+
+**Option B: ESMFold (Fast, synchronous)**
+```
+NvidiaNIM_esmfold(sequence=kinase_domain_sequence)
+└─ Returns: PDB structure (max 1024 AA)
+└─ Use when: Quick assessment needed (~30 sec)
+```
+
+**Report pLDDT Confidence**:
+```markdown
+### 1.4 Structure Prediction Quality
+
+**Method**: AlphaFold2 via NVIDIA NIM
+**Mean pLDDT**: 90.94 (very high confidence)
+
+| Confidence Level | Range | Fraction | Interpretation |
+|------------------|-------|----------|----------------|
+| Very High | ≥90 | 74.3% | Highly reliable |
+| Confident | 70-90 | 16.0% | Reliable |
+| Low | 50-70 | 9.0% | Use caution |
+| Very Low | <50 | 0.7% | Unreliable |
+
+**Key Binding Residue Confidence**:
+| Residue | Function | pLDDT |
+|---------|----------|-------|
+| K745 | ATP binding | 90.0 |
+| T790 | Gatekeeper | 92.3 |
+| M793 | Hinge region | 95.3 |
+| D855 | DFG motif | 89.5 |
+
+*Source: NVIDIA NIM via `NvidiaNIM_alphafold2`*
+```
+
+---
+
+## Phase 2: Known Ligand Mining
+
+### 2.1 ChEMBL Bioactivity Data
+
+```
+1. ChEMBL_get_target_activities(target_chembl_id, limit=500)
+   └─ Filter: standard_type in ["IC50", "Ki", "Kd", "EC50"]
+   └─ Filter: standard_value < 10000 nM
+   └─ Extract: ChEMBL molecule IDs, SMILES, potency values
+
+2. ChEMBL_get_molecule(molecule_chembl_id)  # For top actives
+   └─ Extract: Full molecular data, max_phase, oral flag
+```
+
+**Activity Summary Table**:
+```markdown
+### 2.1 Known Active Compounds (ChEMBL)
+
+**Total Bioactivity Points**: 2,847 (IC50: 1,234 | Ki: 892 | Kd: 456 | EC50: 265)
+**Compounds with IC50 < 100 nM**: 156
+**Approved Drugs for This Target**: 5
+
+| Compound | ChEMBL ID | IC50 (nM) | Max Phase | SMILES (truncated) |
+|----------|-----------|-----------|-----------|-------------------|
+| Erlotinib | CHEMBL553 | 2 | 4 | COc1cc2ncnc(Nc3ccc... |
+| Gefitinib | CHEMBL939 | 5 | 4 | COc1cc2ncnc(Nc3ccc... |
+| [Novel] | CHEMBL123 | 12 | 0 | c1ccc(NC(=O)c2ccc... |
+
+*Source: ChEMBL via `ChEMBL_get_target_activities` (CHEMBL203)*
+```
+
+### 2.2 GtoPdb Interactions
+
+```
+GtoPdb_get_target_interactions(target_id)
+└─ Extract: Ligands with pKi/pIC50, selectivity data
+```
+
+### 2.3 Chemical Probes
+
+```
+OpenTargets_get_chemical_probes_by_target_ensemblID(ensemblId)
+└─ Extract: Validated chemical probes with ratings
+```
+
+**Output for Report**:
+```markdown
+### 2.3 Chemical Probes
+
+| Probe | Target | Rating | Use | Caveat | Source |
+|-------|--------|--------|-----|--------|--------|
+| Probe-X | EGFR | ★★★★ | In vivo | None | Chemical Probes Portal |
+| Probe-Y | EGFR | ★★★☆ | In vitro | Off-target kinase activity | Open Targets |
+
+**Recommended Probe for Target Validation**: Probe-X (highest rating, validated in vivo)
+```
+
+### 2.4 SAR Analysis from Actives
+
+Identify common scaffolds and SAR trends:
+
+```markdown
+### 2.4 Structure-Activity Relationships
+
+**Core Scaffolds Identified**:
+1. **4-Anilinoquinazoline** (34 compounds, IC50 range: 2-500 nM)
+   - N1 position: Aryl preferred
+   - C6/C7: Methoxy groups improve potency
+   
+2. **Pyrimidine-amine** (12 compounds, IC50 range: 15-800 nM)
+   - Less potent than quinazolines
+   - Better selectivity profile
+
+**Key SAR Insights**:
+- Halogen at meta position of aniline increases potency 3-5x
+- C7 ethoxy group critical for binding (H-bond to M793)
+```
+
+### 2.5 BindingDB Affinity Data (NEW)
+
+BindingDB provides experimental binding affinity data complementary to ChEMBL:
+
+```python
+def get_bindingdb_ligands(tu, uniprot_id, affinity_cutoff=10000):
+    """
+    Get ligands from BindingDB with measured affinities.
+    
+    BindingDB advantages:
+    - May have compounds not in ChEMBL
+    - Different affinity types (Ki, IC50, Kd)
+    - Direct literature links
+    """
+    
+    result = tu.tools.BindingDB_get_ligands_by_uniprot(
+        uniprot=uniprot_id,
+        affinity_cutoff=affinity_cutoff  # nM
+    )
+    
+    if result:
+        ligands = []
+        for entry in result:
+            ligands.append({
+                'smiles': entry.get('smile'),
+                'affinity_type': entry.get('affinity_type'),
+                'affinity_nM': entry.get('affinity'),
+                'pmid': entry.get('pmid'),
+                'monomer_id': entry.get('monomerid')
+            })
+        
+        # Sort by potency
+        ligands.sort(key=lambda x: float(x['affinity_nM']) if x['affinity_nM'] else 1e6)
+        return ligands[:50]  # Top 50
+    
+    return []
+
+def find_compound_polypharmacology(tu, smiles, similarity_cutoff=0.85):
+    """Find off-target interactions for selectivity analysis."""
+    
+    targets = tu.tools.BindingDB_get_targets_by_compound(
+        smiles=smiles,
+        similarity_cutoff=similarity_cutoff
+    )
+    
+    return targets  # Other proteins this compound may bind
+```
+
+**BindingDB Output for Report**:
+```markdown
+### 2.5 Additional Ligands (BindingDB) (NEW)
+
+**Total Unique Ligands**: 89 (non-overlapping with ChEMBL)
+**Most Potent**: 0.3 nM Ki
+
+| SMILES | Affinity Type | Value (nM) | PMID | BindingDB ID |
+|--------|---------------|------------|------|--------------|
+| CC(C)Cc1ccc... | Ki | 0.3 | 15737014 | 12345 |
+| COc1cc2ncnc... | IC50 | 2.1 | 16460808 | 12346 |
+
+**Novel Scaffolds from BindingDB**: 3 scaffolds not seen in ChEMBL data
+
+*Source: BindingDB via `BindingDB_get_ligands_by_uniprot`*
+```
+
+### 2.6 PubChem BioAssay Screening Data (NEW)
+
+PubChem BioAssay provides HTS screening results and dose-response data:
+
+```python
+def get_pubchem_assays_for_target(tu, gene_symbol):
+    """
+    Get bioassays and active compounds from PubChem.
+    
+    Advantages:
+    - HTS data not in ChEMBL
+    - NIH-funded screening programs (MLPCN)
+    - Dose-response curves for IC50 calculation
+    """
+    
+    # Search assays targeting this gene
+    assays = tu.tools.PubChem_search_assays_by_target_gene(
+        gene_symbol=gene_symbol
+    )
+    
+    results = {
+        'assays': [],
+        'total_active_compounds': 0
+    }
+    
+    if assays.get('data', {}).get('aids'):
+        for aid in assays['data']['aids'][:10]:  # Top 10 assays
+            # Get assay summary
+            summary = tu.tools.PubChem_get_assay_summary(aid=aid)
+            
+            # Get active compounds
+            actives = tu.tools.PubChem_get_assay_active_compounds(aid=aid)
+            active_cids = actives.get('data', {}).get('cids', [])
+            
+            results['assays'].append({
+                'aid': aid,
+                'summary': summary.get('data', {}),
+                'active_count': len(active_cids)
+            })
+            results['total_active_compounds'] += len(active_cids)
+    
+    return results
+
+def get_dose_response_data(tu, aid):
+    """Get dose-response curves for IC50/EC50 determination."""
+    
+    dr_data = tu.tools.PubChem_get_assay_dose_response(aid=aid)
+    return dr_data
+
+def get_compound_bioactivity_profile(tu, cid):
+    """Get all bioactivity data for a compound."""
+    
+    profile = tu.tools.PubChem_get_compound_bioactivity(cid=cid)
+    return profile
+```
+
+**PubChem BioAssay Output for Report**:
+```markdown
+### 2.6 PubChem HTS Screening Data (NEW)
+
+**Assays Found**: 45
+**Total Active Compounds Across Assays**: ~1,200
+
+| AID | Assay Type | Active Compounds | Target | Description |
+|-----|------------|------------------|--------|-------------|
+| 504526 | HTS | 234 | EGFR | qHTS inhibition screen |
+| 1053104 | Dose-response | 12 | EGFR kinase | Confirmatory IC50 |
+| 651564 | Cellular | 8 | EGFR | Cell proliferation assay |
+
+**Novel Actives** (not in ChEMBL/BindingDB):
+- CID 12345678: Active in AID 504526, IC50 = 45 nM
+- CID 23456789: Active in AID 1053104, IC50 = 120 nM
+
+*Source: PubChem via `PubChem_search_assays_by_target_gene`, `PubChem_get_assay_active_compounds`*
+```
+
+**Why Use Both BindingDB and PubChem**:
+| Source | Strengths | Best For |
+|--------|-----------|----------|
+| **ChEMBL** | Curated, standardized, SAR data | Primary ligand source |
+| **BindingDB** | Direct affinity measurements | Ki/Kd values, PMIDs |
+| **PubChem BioAssay** | HTS data, NIH screens | Novel scaffolds, broad coverage |
+
+---
+
+## Phase 3: Structure Analysis
+
+### 3.1 PDB Structure Retrieval
+
+```
+1. PDB_search_similar_structures(query=uniprot_accession, type="sequence")
+   └─ Extract: PDB IDs with ligands
+   
+2. get_protein_metadata_by_pdb_id(pdb_id)
+   └─ Extract: Resolution, method, ligand codes
+   
+3. alphafold_get_prediction(accession=uniprot_accession)
+   └─ Extract: Predicted structure (if no experimental)
+```
+
+### 3.1b EMDB Cryo-EM Structures (NEW)
+
+**Prioritize EMDB for**: Membrane proteins (GPCRs, ion channels), large complexes, targets with multiple conformational states.
+
+```python
+def get_cryoem_structures(tu, target_name, uniprot_accession):
+    """Get cryo-EM structures for membrane targets."""
+    
+    # Search EMDB
+    emdb_results = tu.tools.emdb_search(
+        query=f"{target_name} membrane receptor"
+    )
+    
+    structures = []
+    for entry in emdb_results[:5]:
+        details = tu.tools.emdb_get_entry(entry_id=entry['emdb_id'])
+        
+        # Get associated PDB model (essential for docking)
+        pdb_models = details.get('pdb_ids', [])
+        
+        structures.append({
+            'emdb_id': entry['emdb_id'],
+            'resolution': entry.get('resolution', 'N/A'),
+            'title': entry.get('title', 'N/A'),
+            'conformational_state': details.get('state', 'Unknown'),
+            'pdb_models': pdb_models
+        })
+    
+    return structures
+```
+
+**When to use cryo-EM over X-ray**:
+| Target Type | Prefer cryo-EM? | Reason |
+|-------------|-----------------|--------|
+| GPCR | Yes | Native membrane conformation |
+| Ion channel | Yes | Multiple functional states |
+| Receptor-ligand complex | Yes | Physiological state |
+| Kinase | Usually X-ray | Higher resolution typically |
+
+**Structure Summary**:
+```markdown
+### 3.1 Available Structures
+
+| PDB ID | Resolution | Method | Ligand | Affinity | State |
+|--------|------------|--------|--------|----------|-------|
+| 1M17 | 2.6 Å | X-ray | Erlotinib | Ki=0.4 nM | Active |
+| 4HJO | 2.1 Å | X-ray | Lapatinib | Ki=3 nM | Inactive |
+| AF-P00533 | - | Predicted | None | - | - |
+
+### 3.1b Cryo-EM Structures (EMDB)
+
+| EMDB ID | Resolution | PDB Model | Conformation | Ligand |
+|---------|------------|-----------|--------------|--------|
+| EMD-12345 | 3.2 Å | 7ABC | Active | Agonist |
+| EMD-23456 | 3.5 Å | 8DEF | Inactive | Antagonist |
+
+**Best Structure for Docking**: 1M17 (high resolution, relevant ligand)
+*Source: RCSB PDB, EMDB, AlphaFold DB*
+```
+
+### 3.2 Binding Pocket Analysis
+
+```
+get_binding_affinity_by_pdb_id(pdb_id)
+└─ Extract: Binding affinities for co-crystallized ligands
+```
+
+**Output for Report**:
+```markdown
+### 3.2 Binding Pocket Characterization
+
+**Pocket Volume**: ~850 ų (well-defined)
+**Key Interaction Residues**:
+- **Hinge region**: M793 (backbone H-bond donor/acceptor)
+- **Gatekeeper**: T790 (small residue, allows access)
+- **DFG motif**: D855 (active conformation)
+- **Selectivity pocket**: L788, G796 (unique to EGFR)
+
+**Druggability Assessment**: High (enclosed pocket, conserved interactions)
+```
+
+---
+
+## Phase 3.5: Docking Validation (NVIDIA NIM)
+
+Validate structure and score compounds using molecular docking.
+
+**Requires**: `NVIDIA_API_KEY` environment variable
+
+### 3.5.1 Reference Compound Docking
+
+Dock a known inhibitor to validate the structure captures the binding pocket correctly.
+
+**Option A: DiffDock (Blind docking, PDB + SDF input)**
+```
+NvidiaNIM_diffdock(
+    protein=pdb_content,        # PDB text content
+    ligand=reference_sdf,       # SDF/MOL2 content
+    num_poses=10
+)
+└─ Returns: Docking poses with confidence scores
+└─ Use: When you have PDB structure and ligand SDF file
+```
+
+**Option B: Boltz2 (From sequence + SMILES)**
+```
+NvidiaNIM_boltz2(
+    polymers=[{"molecule_type": "protein", "sequence": kinase_sequence}],
+    ligands=[{"smiles": "COc1cc2ncnc(Nc3ccc(C#C)cc3)c2cc1OCCOC"}],
+    sampling_steps=50,
+    diffusion_samples=1
+)
+└─ Returns: Protein-ligand complex structure
+└─ Use: When starting from SMILES, no SDF needed
+```
+
+### 3.5.2 Docking Score Interpretation
+
+| Score vs Reference | Priority | Symbol |
+|--------------------|----------|--------|
+| Higher than reference | Top priority | ★★★★ |
+| Within 5% of reference | High priority | ★★★ |
+| Within 20% of reference | Moderate priority | ★★☆ |
+| >20% lower | Low priority | ★☆☆ |
+
+**Report Format**:
+```markdown
+### 3.5 Docking Validation Results
+
+**Reference Compound**: Erlotinib
+**Method**: DiffDock via NVIDIA NIM
+
+| Metric | Value | Interpretation |
+|--------|-------|----------------|
+| Best Pose Confidence | 0.906 | Excellent |
+| Steric Clashes | None | Clean binding pose |
+
+**Validation Status**: ✓ Structure captures binding pocket correctly
+
+*Source: NVIDIA NIM via `NvidiaNIM_diffdock`*
+```
+
+---
+
+## Phase 4: Compound Expansion
+
+### 4.1 Similarity Search
+
+Starting from top actives, expand chemical space:
+
+```
+1. ChEMBL_search_similar_molecules(molecule=top_active_smiles, similarity=70)
+   └─ Extract: Similar compounds not yet tested on target
+   
+2. PubChem_search_compounds_by_similarity(smiles, threshold=0.7)
+   └─ Extract: PubChem CIDs with similar structures
+```
+
+**Strategy**:
+- Use 3-5 diverse actives as seeds
+- Similarity threshold: 70-85% (balance novelty vs. activity)
+- Prioritize compounds NOT in ChEMBL bioactivity for target
+
+### 4.2 Substructure Search
+
+```
+1. ChEMBL_search_substructure(smiles=core_scaffold)
+   └─ Extract: Compounds containing scaffold
+   
+2. PubChem_search_compounds_by_substructure(smiles=core_scaffold)
+   └─ Extract: Additional scaffold-containing compounds
+```
+
+### 4.3 Cross-Database Mining
+
+```
+1. STITCH_get_chemical_protein_interactions(identifier=target_gene)
+   └─ Extract: Additional chemical-protein links
+   
+2. DGIdb_get_drug_gene_interactions(genes=[gene_symbol])
+   └─ Extract: Approved/investigational drugs
+```
+
+**Output for Report**:
+```markdown
+### 4. Compound Expansion Results
+
+**Starting Seeds**: 5 diverse actives (IC50 < 100 nM)
+**Similarity Expansion**: 847 compounds (70% threshold)
+**Substructure Search**: 234 scaffold matches
+**Cross-Database**: 45 additional hits
+
+**After Deduplication**: 923 unique candidate compounds
+
+| Source | Compounds | Already Tested | Novel Candidates |
+|--------|-----------|----------------|------------------|
+| ChEMBL similarity | 456 | 234 | 222 |
+| PubChem similarity | 391 | 156 | 235 |
+| ChEMBL substructure | 178 | 89 | 89 |
+| STITCH | 45 | 23 | 22 |
+| **Total Unique** | **923** | **355** | **568** |
+```
+
+### 4.4 De Novo Molecule Generation (NVIDIA NIM)
+
+When database mining yields insufficient candidates, generate novel molecules.
+
+**Requires**: `NVIDIA_API_KEY` environment variable
+
+**Option A: GenMol (Scaffold Hopping with Masked Regions)**
+```
+NvidiaNIM_genmol(
+    smiles="COc1cc2ncnc(Nc3ccc([*{3-8}])c([*{1-3}])c3)c2cc1OCCCN1CCOCC1",
+    num_molecules=100,
+    temperature=2.0,
+    scoring="QED"
+)
+└─ Input: SMILES with [*{min-max}] masked regions
+└─ Output: Generated molecules with QED/LogP scores
+└─ Use: Explore specific positions while keeping scaffold
+```
+
+**Mask Design Strategy**:
+| Position | Mask | Purpose |
+|----------|------|---------|
+| Aniline substituent | `[*{1-3}]` | Small groups (halogen, methyl) |
+| Solubilizing group | `[*{5-10}]` | Morpholine, piperazine variants |
+| Linker region | `[*{3-6}]` | Spacer variations |
+
+**Example Masked SMILES for EGFR**:
+```
+# Keep quinazoline core, vary aniline and tail
+COc1cc2ncnc(Nc3ccc([*{1-3}])c([*{1-3}])c3)c2cc1[*{5-12}]
+```
+
+**Option B: MolMIM (Controlled Generation from Reference)**
+```
+NvidiaNIM_molmim(
+    smi="COc1cc2ncnc(Nc3ccc(Cl)cc3)c2cc1OCCN1CCOCC1",
+    num_molecules=50,
+    algorithm="CMA-ES"
+)
+└─ Input: Reference SMILES (known active)
+└─ Output: Optimized analogs with property scores
+└─ Use: Generate close analogs of top actives
+```
+
+**Generation Workflow**:
+1. Identify top 3-5 actives from Phase 2
+2. Design masked SMILES for GenMol OR use as reference for MolMIM
+3. Generate 50-100 molecules per seed
+4. Pass generated molecules to Phase 5 (ADMET filtering)
+5. Dock survivors in Phase 6 for final ranking
+
+**Report Format**:
+```markdown
+### 4.4 De Novo Generation Results
+
+**Method**: GenMol via NVIDIA NIM
+**Seed Scaffold**: 4-anilinoquinazoline (from erlotinib)
+**Masked Positions**: Aniline (3,4), solubilizing tail
+
+| Metric | Value |
+|--------|-------|
+| Molecules Generated | 100 |
+| Passing Lipinski | 95 (95%) |
+| Mean QED Score | 0.72 |
+| Unique Scaffolds | 12 |
+
+**Top Generated Compounds**:
+| ID | SMILES | QED | LogP | Novelty |
+|----|--------|-----|------|---------|
+| GEN-001 | COc1cc2ncnc(Nc3ccc(Cl)c(Cl)c3)c2cc1OCCCN1CCOCC1 | 0.81 | 4.2 | Novel substitution |
+| GEN-002 | COc1cc2ncnc(Nc3ccc(C#N)c(F)c3)c2cc1OCCCN1CCOCC1 | 0.78 | 3.8 | Novel substitution |
+
+*Source: NVIDIA NIM via `NvidiaNIM_genmol`*
+```
+
+---
+
+## Phase 5: ADMET Filtering
+
+### 5.1 Physicochemical Properties
+
+```
+ADMETAI_predict_physicochemical_properties(smiles=[compound_list])
+└─ Filter: Lipinski violations ≤ 1
+└─ Filter: QED > 0.3
+└─ Filter: MW 200-600
+```
+
+### 5.2 ADMET Endpoints
+
+```
+1. ADMETAI_predict_bioavailability(smiles=[compound_list])
+   └─ Filter: Oral bioavailability > 0.3
+   
+2. ADMETAI_predict_toxicity(smiles=[compound_list])
+   └─ Filter: AMES < 0.5, hERG < 0.5, DILI < 0.5
+   
+3. ADMETAI_predict_CYP_interactions(smiles=[compound_list])
+   └─ Flag: CYP3A4 inhibitors (drug interaction risk)
+```
+
+### 5.3 Structural Alerts
+
+```
+ChEMBL_search_compound_structural_alerts(smiles=compound_smiles)
+└─ Flag: PAINS, reactive groups, toxicophores
+```
+
+**ADMET Filter Summary**:
+```markdown
+### 5. ADMET Filtering Results
+
+| Filter Stage | Input | Passed | Failed | Pass Rate |
+|--------------|-------|--------|--------|-----------|
+| Physicochemical (Lipinski) | 568 | 456 | 112 | 80% |
+| Drug-likeness (QED > 0.3) | 456 | 398 | 58 | 87% |
+| Bioavailability (> 0.3) | 398 | 312 | 86 | 78% |
+| Toxicity filters | 312 | 267 | 45 | 86% |
+| Structural alerts | 267 | 234 | 33 | 88% |
+| **Final Candidates** | **568** | **234** | **334** | **41%** |
+
+**Common Failure Reasons**:
+1. High molecular weight (>600): 67 compounds
+2. Low predicted bioavailability: 86 compounds
+3. hERG liability: 28 compounds
+4. PAINS alerts: 18 compounds
+```
+
+---
+
+## Phase 6: Candidate Prioritization
+
+### 6.1 Scoring Framework
+
+Score each candidate on multiple dimensions:
+
+| Dimension | Weight | Scoring Criteria |
+|-----------|--------|------------------|
+| **Structural Similarity** | 25% | Tanimoto to actives (0.7-1.0 → 1-5) |
+| **Novelty** | 20% | Not in ChEMBL bioactivity = +2; Novel scaffold = +3 |
+| **ADMET Score** | 25% | Composite of property predictions |
+| **Synthesis Feasibility** | 15% | SA score (1-10), commercial availability |
+| **Scaffold Diversity** | 15% | Cluster representative bonus |
+
+### 6.2 Synthesis Feasibility
+
+```markdown
+### 6.2 Synthesis Feasibility Assessment
+
+| Candidate | SA Score | Commercial | Estimated Steps | Flag |
+|-----------|----------|------------|-----------------|------|
+| Compound-1 | 2.3 | Yes (Enamine) | 0 | ★★★ |
+| Compound-2 | 3.5 | Building block | 2-3 | ★★☆ |
+| Compound-3 | 5.8 | No | 6-8 | ★☆☆ |
+
+**SA Score Interpretation**:
+- 1-3: Easy synthesis
+- 3-5: Moderate complexity
+- 5-10: Challenging synthesis
+```
+
+### 6.3 Final Prioritized List
+
+```markdown
+### 6.3 Top 20 Candidate Compounds
+
+| Rank | ID | SMILES | Sim. Score | ADMET | Novelty | Overall | Rationale |
+|------|-----|--------|------------|-------|---------|---------|-----------|
+| 1 | CPD-001 | Cc1ccc... | 0.82 | 4.5 | Novel scaffold | 4.2 | High similarity, clean ADMET |
+| 2 | CPD-002 | COc1cc... | 0.78 | 4.3 | Not tested | 4.0 | Quinazoline analog |
+| 3 | CPD-003 | Nc1ccc... | 0.75 | 4.1 | Novel core | 3.9 | New chemotype |
+| ... | ... | ... | ... | ... | ... | ... | ... |
+
+**Scaffold Diversity**: 7 distinct scaffolds in top 20
+**Commercial Availability**: 12/20 available for purchase
+**Estimated Hit Rate**: 15-25% (based on similarity to actives)
+```
+
+---
+
+## Phase 6.5: Literature Evidence (NEW)
+
+### 6.5.1 Literature Search for Validation
+
+Search literature to validate candidate compounds and understand target context.
+
+```python
+def search_binder_literature(tu, target_name, compound_scaffolds):
+    """Search literature for compound and target evidence."""
+    
+    # PubMed: Published SAR studies
+    sar_papers = tu.tools.PubMed_search_articles(
+        query=f"{target_name} inhibitor SAR structure-activity",
+        limit=30
+    )
+    
+    # BioRxiv: Latest unpublished findings
+    preprints = tu.tools.BioRxiv_search_preprints(
+        query=f"{target_name} small molecule discovery",
+        limit=15
+    )
+    
+    # MedRxiv: Clinical data on inhibitors
+    clinical = tu.tools.MedRxiv_search_preprints(
+        query=f"{target_name} inhibitor clinical trial",
+        limit=10
+    )
+    
+    # Citation analysis for key papers
+    key_papers = sar_papers[:10]
+    for paper in key_papers:
+        citation = tu.tools.openalex_search_works(
+            query=paper['title'],
+            limit=1
+        )
+        paper['citations'] = citation[0].get('cited_by_count', 0) if citation else 0
+    
+    return {
+        'published_sar': sar_papers,
+        'preprints': preprints,
+        'clinical_preprints': clinical,
+        'high_impact_papers': sorted(key_papers, key=lambda x: x.get('citations', 0), reverse=True)
+    }
+```
+
+### 6.5.2 Output for Report
+
+```markdown
+## 6.5 Literature Evidence
+
+### Published SAR Studies
+
+| PMID | Title | Year | Key Insight |
+|------|-------|------|-------------|
+| 34567890 | Discovery of novel EGFR inhibitors... | 2024 | C7 substitution critical |
+| 33456789 | Structure-activity relationship of... | 2023 | Fluorine improves potency |
+
+### Recent Preprints (⚠️ Not Peer-Reviewed)
+
+| Source | Title | Posted | Relevance |
+|--------|-------|--------|-----------|
+| BioRxiv | Novel scaffolds for EGFR... | 2024-02 | New chemotype discovery |
+| MedRxiv | Clinical activity of... | 2024-01 | Phase 2 results |
+
+### High-Impact References
+
+| PMID | Citations | Title |
+|------|-----------|-------|
+| 32123456 | 523 | Landmark EGFR inhibitor study... |
+| 31234567 | 312 | Comprehensive SAR analysis... |
+
+*Source: PubMed, BioRxiv, MedRxiv, OpenAlex*
+```
+
+---
+
+## Report Template
+
+**File**: `[TARGET]_binder_discovery_report.md`
+
+```markdown
+# Small Molecule Binder Discovery: [TARGET]
+
+**Generated**: [Date] | **Query**: [Original query] | **Status**: In Progress
+
+---
+
+## Executive Summary
+[Researching...]
+
+---
+
+## 1. Target Validation
+### 1.1 Target Identifiers
+[Researching...]
+### 1.2 Druggability Assessment
+[Researching...]
+### 1.3 Binding Site Analysis
+[Researching...]
+
+---
+
+## 2. Known Ligand Landscape
+### 2.1 ChEMBL Bioactivity Summary
+[Researching...]
+### 2.2 Approved Drugs & Clinical Compounds
+[Researching...]
+### 2.3 Chemical Probes
+[Researching...]
+### 2.4 SAR Insights
+[Researching...]
+
+---
+
+## 3. Structural Information
+### 3.1 Available Structures
+[Researching...]
+### 3.2 Binding Pocket Analysis
+[Researching...]
+### 3.3 Key Interactions
+[Researching...]
+
+---
+
+## 4. Compound Expansion
+### 4.1 Similarity Search Results
+[Researching...]
+### 4.2 Substructure Search Results
+[Researching...]
+### 4.3 Cross-Database Mining
+[Researching...]
+
+---
+
+## 5. ADMET Filtering
+### 5.1 Physicochemical Filters
+[Researching...]
+### 5.2 ADMET Predictions
+[Researching...]
+### 5.3 Structural Alerts
+[Researching...]
+### 5.4 Filter Summary
+[Researching...]
+
+---
+
+## 6. Candidate Prioritization
+### 6.1 Scoring Methodology
+[Researching...]
+### 6.2 Synthesis Feasibility
+[Researching...]
+### 6.3 Top 20 Candidates
+[Researching...]
+
+---
+
+## 7. Recommendations
+### 7.1 Immediate Actions
+[Researching...]
+### 7.2 Experimental Validation Plan
+[Researching...]
+### 7.3 Backup Strategies
+[Researching...]
+
+---
+
+## 8. Data Gaps & Limitations
+[Researching...]
+
+---
+
+## 9. Data Sources
+[Will be populated as research progresses...]
+
+---
+
+## 10. Methods Summary
+
+| Step | Tool | Purpose |
+|------|------|---------|
+| Sequence retrieval | UniProt_search | Get protein sequence |
+| Structure prediction | NvidiaNIM_alphafold2 / NvidiaNIM_esmfold | 3D structure with pLDDT |
+| Docking validation | NvidiaNIM_diffdock / NvidiaNIM_boltz2 | Validate binding pocket |
+| Known ligands | ChEMBL_get_target_activities | Bioactivity data |
+| Similarity search | ChEMBL_search_similar_molecules | Expand chemical space |
+| De novo generation | NvidiaNIM_genmol / NvidiaNIM_molmim | Novel molecule design |
+| ADMET filtering | ADMETAI_predict_* | Drug-likeness assessment |
+| Candidate docking | NvidiaNIM_diffdock / NvidiaNIM_boltz2 | Final scoring |
+```
+
+---
+
+## Evidence Grading
+
+| Tier | Symbol | Description | Example |
+|------|--------|-------------|---------|
+| **T0** | ★★★★ | Docking score > reference inhibitor | Better than erlotinib |
+| **T1** | ★★★ | Experimental IC50/Ki < 100 nM | ChEMBL bioactivity |
+| **T2** | ★★☆ | Docking within 5% of reference OR IC50 100-1000 nM | High priority |
+| **T3** | ★☆☆ | Structural similarity > 80% to T1 | Predicted active |
+| **T4** | ☆☆☆ | Similarity 70-80%, scaffold match | Lower confidence |
+| **T5** | ○○○ | Generated molecule, ADMET-passed, no docking | Speculative |
+
+**Docking-Enhanced Grading**: When NVIDIA NIM docking is available, compounds gain evidence:
+- Docking > reference → upgrade to T0 (★★★★)
+- Docking within 5% → upgrade to T2 (★★☆)
+- Docking within 20% → maintain current tier
+- Docking >20% worse → downgrade one tier
+
+Apply to all candidate compounds:
+```markdown
+| Compound | Evidence | Docking vs Ref | Rationale |
+|----------|----------|----------------|-----------|
+| CPD-001 | ★★★★ | +8.3% | 85% similar, docking > erlotinib |
+| CPD-002 | ★★★ | -2.1% | IC50=45nM, validated by docking |
+| CPD-003 | ★★☆ | -4.5% | 78% similar, good docking |
+| GEN-001 | ★☆☆ | -15% | Generated, ADMET-passed |
+```
+
+---
+
+## Mandatory Completeness Checklist
+
+### Phase 1: Target Validation
+- [ ] UniProt accession resolved
+- [ ] ChEMBL target ID obtained
+- [ ] Druggability assessed (≥2 sources)
+- [ ] Target class identified
+- [ ] Binding site information (or "No structural data")
+
+### Phase 2: Known Ligands
+- [ ] ChEMBL activities queried (≥100 or all available)
+- [ ] Activity statistics (count, potency range)
+- [ ] Top 10 actives listed with IC50
+- [ ] Chemical probes identified (or "None available")
+- [ ] SAR insights summarized
+
+### Phase 3: Structure
+- [ ] PDB structures listed (or "No experimental structure")
+- [ ] Best structure for docking identified
+- [ ] Binding pocket described (or "Predicted from AlphaFold")
+
+### Phase 4: Expansion
+- [ ] ≥3 seed compounds used
+- [ ] Similarity search completed (≥100 results or exhausted)
+- [ ] Substructure search completed
+- [ ] Deduplicated candidate count reported
+
+### Phase 5: ADMET
+- [ ] Physicochemical filters applied
+- [ ] Toxicity predictions run
+- [ ] Structural alerts checked
+- [ ] Filter funnel table included
+
+### Phase 6: Prioritization
+- [ ] ≥20 candidates ranked (or all if fewer)
+- [ ] Scoring methodology explained
+- [ ] Synthesis feasibility assessed
+- [ ] Scaffold diversity noted
+
+### Phase 7: Recommendations
+- [ ] ≥3 immediate actions listed
+- [ ] Experimental validation plan outlined
+- [ ] Data gaps aggregated
+
+---
+
+## Tool Reference by Phase
+
+### Phase 1: Target Validation
+| Tool | Purpose |
+|------|---------|
+| `UniProt_search` | Resolve UniProt accession |
+| `MyGene_query_genes` | Get Ensembl/NCBI IDs |
+| `ChEMBL_search_targets` | Get ChEMBL target ID |
+| `OpenTargets_get_target_tractability_by_ensemblID` | Tractability assessment |
+| `DGIdb_get_gene_druggability` | Druggability categories |
+| `ChEMBL_search_binding_sites` | Binding site info |
+| `InterPro_get_protein_domains` | Domain architecture |
+
+### Phase 2: Known Ligands
+| Tool | Purpose |
+|------|---------|
+| `ChEMBL_get_target_activities` | Bioactivity data |
+| `ChEMBL_get_molecule` | Molecule details |
+| `GtoPdb_get_target_interactions` | Pharmacology data |
+| `OpenTargets_get_chemical_probes_by_target_ensemblID` | Chemical probes |
+| `OpenTargets_get_associated_drugs_by_target_ensemblID` | Known drugs |
+
+### Phase 1.4: Structure Prediction (NVIDIA NIM)
+| Tool | Purpose |
+|------|---------|
+| `NvidiaNIM_alphafold2` | High-accuracy structure prediction with pLDDT |
+| `NvidiaNIM_esmfold` | Fast structure prediction (max 1024 AA) |
+| `NvidiaNIM_msa_search` | MSA generation for AlphaFold |
+
+### Phase 3: Structure
+| Tool | Purpose |
+|------|---------|
+| `PDB_search_similar_structures` | Find PDB structures |
+| `get_protein_metadata_by_pdb_id` | Structure metadata |
+| `get_binding_affinity_by_pdb_id` | Ligand affinities |
+| `alphafold_get_prediction` | Predicted structure (AlphaFold DB) |
+| `get_ligand_smiles_by_chem_comp_id` | Ligand structures |
+| `emdb_search` | Search cryo-EM structures (NEW) |
+| `emdb_get_entry` | Get EMDB entry details (NEW) |
+
+### Phase 3.5: Docking Validation (NVIDIA NIM)
+| Tool | Purpose |
+|------|---------|
+| `NvidiaNIM_diffdock` | Blind molecular docking (PDB + SDF) |
+| `NvidiaNIM_boltz2` | Protein-ligand complex (sequence + SMILES) |
+
+### Phase 4: Expansion
+| Tool | Purpose |
+|------|---------|
+| `ChEMBL_search_similar_molecules` | Similarity search |
+| `PubChem_search_compounds_by_similarity` | PubChem similarity |
+| `ChEMBL_search_substructure` | Substructure search |
+| `PubChem_search_compounds_by_substructure` | PubChem substructure |
+| `STITCH_get_chemical_protein_interactions` | Cross-database |
+
+### Phase 4.4: De Novo Generation (NVIDIA NIM)
+| Tool | Purpose |
+|------|---------|
+| `NvidiaNIM_genmol` | Scaffold hopping with masked regions |
+| `NvidiaNIM_molmim` | Controlled generation from reference |
+
+### Phase 5: ADMET
+| Tool | Purpose |
+|------|---------|
+| `ADMETAI_predict_physicochemical_properties` | Drug-likeness |
+| `ADMETAI_predict_bioavailability` | Oral absorption |
+| `ADMETAI_predict_toxicity` | Toxicity flags |
+| `ADMETAI_predict_CYP_interactions` | CYP liabilities |
+| `ChEMBL_search_compound_structural_alerts` | PAINS, alerts |
+
+### Phase 6: Candidate Docking (NVIDIA NIM)
+| Tool | Purpose |
+|------|---------|
+| `NvidiaNIM_diffdock` | Score all candidates by docking |
+| `NvidiaNIM_boltz2` | Alternative docking from SMILES |
+
+### Phase 6.5: Literature Evidence (NEW)
+| Tool | Purpose |
+|------|---------|
+| `PubMed_search_articles` | Published SAR studies |
+| `BioRxiv_search_preprints` | Latest biology preprints |
+| `MedRxiv_search_preprints` | Clinical preprints |
+| `openalex_search_works` | Citation analysis |
+| `SemanticScholar_search` | AI-ranked papers |
+
+---
+
+## Fallback Chains
+
+| Primary Tool | Fallback 1 | Fallback 2 | Use When |
+|--------------|------------|------------|----------|
+| `ChEMBL_get_target_activities` | `GtoPdb_get_target_interactions` | `PubChem_search_assays` | No ChEMBL data |
+| `ChEMBL_search_similar_molecules` | `PubChem_search_compounds_by_similarity` | `STITCH_get_chemical_protein_interactions` | ChEMBL exhausted |
+| `PDB_search_similar_structures` | `NvidiaNIM_alphafold2` | `alphafold_get_prediction` | No PDB structure |
+| `alphafold_get_prediction` | `NvidiaNIM_alphafold2` | `NvidiaNIM_esmfold` | AlphaFold DB unavailable |
+| `NvidiaNIM_alphafold2` | `NvidiaNIM_esmfold` | `alphafold_get_prediction` | AlphaFold2 NIM error |
+| `NvidiaNIM_diffdock` | `NvidiaNIM_boltz2` | Skip docking, use similarity | Docking error |
+| `NvidiaNIM_genmol` | `NvidiaNIM_molmim` | Manual scaffold hopping | Generation error |
+| `OpenTargets_get_target_tractability` | `DGIdb_get_gene_druggability` | Document "Unknown" | Open Targets error |
+| `ADMETAI_*` | SwissADME tools | Basic Lipinski | Invalid SMILES |
+| `PDB_search_similar_structures` | `emdb_search` + PDB | `NvidiaNIM_alphafold2` | Membrane proteins |
+| `PubMed_search_articles` | `openalex_search_works` | `SemanticScholar_search` | Literature search |
+| `BioRxiv_search_preprints` | `MedRxiv_search_preprints` | Skip preprints | Preprint sources |
+
+**NVIDIA NIM API Key Required**: Tools with `NvidiaNIM_` prefix require `NVIDIA_API_KEY` environment variable. Check availability at start:
+```python
+import os
+nvidia_available = bool(os.environ.get("NVIDIA_API_KEY"))
+# If not available, fall back to non-NIM alternatives
+```
+
+---
+
+## Common Use Cases
+
+### Well-Characterized Target
+User: "Find novel binders for EGFR"
+→ Rich ChEMBL data; focus on novel scaffolds, selectivity, ADMET
+
+### Novel Target
+User: "Find small molecules for [new target with no known ligands]"
+→ Limited bioactivity; rely on structure-based assessment, similar target ligands
+
+### Lead Optimization
+User: "Find analogs of compound X for target Y"
+→ Deep similarity search around specific compound; focus on SAR
+
+### Selectivity Challenge
+User: "Find selective inhibitors for kinase X vs kinase Y"
+→ Include selectivity analysis; filter by off-target predictions
+
+---
+
+## When NOT to Use This Skill
+
+- **Drug research** → Use tooluniverse-drug-research (existing drug profiling)
+- **Target research only** → Use tooluniverse-target-research
+- **Single compound ADMET** → Call ADMET tools directly
+- **Literature search** → Use tooluniverse-literature-deep-research
+- **Protein structure only** → Use tooluniverse-protein-structure-retrieval
+
+Use this skill for **discovering new compounds** for a protein target.
+
+---
+
+## Additional Resources
+
+- **Checklist**: [CHECKLIST.md](CHECKLIST.md) - Pre-delivery verification
+- **Examples**: [EXAMPLES.md](EXAMPLES.md) - Detailed workflow examples
+- **Tool corrections**: [TOOLS_REFERENCE.md](TOOLS_REFERENCE.md) - Parameter corrections