Drug Discovery — Drug discovery: ChEMBL search, drug-likeness, interactions
Drug Discovery — Drug discovery: ChEMBL search, drug-likeness, interactions
Start with meaning, then move to detail.
This lesson explains Drug Discovery — Drug discovery: ChEMBL search, drug-likeness, interactions as part of extending Hermes and connecting external tools. You will learn what it does, when it matters, and the smallest safe test that proves it works.
If you are new, do not memorize names. Focus on three questions: what problem does this solve, what access does it need, and how can you verify the result?
For practice, inspect the first example, identify its effects, run it on test data, and compare the result with the source claim.
For advanced readers, inspect Skill metadata, Reference: full SKILL.md, Core Workflows, then verify failure modes and version compatibility.
Complete installation and one successful task before adding new capabilities.
A clear outcome before you read.
- Understand Drug Discovery — Drug discovery: ChEMBL search, drug-likeness, interactions without assumed prior knowledge.
- Separate the source description from what still needs testing in your environment.
- Read the first command and identify its inputs and outputs before copying it.
Short definitions before the details.
- Skill
- An instruction bundle that teaches Hermes a repeatable workflow without necessarily adding an external service.
Drug discovery: ChEMBL search, drug-likeness, interactions
What does the source say, and in what order?
- 01Skill metadata
Start here to understand the core idea or structure.
- 02Reference: full SKILL.md
Read this after the foundation, then connect it to the previous step.
- 03Core Workflows
Read this after the foundation, then connect it to the previous step.
- 041 — Bioactive Compound Search (ChEMBL)
Read this after the foundation, then connect it to the previous step.
- 052 — Drug-Likeness Calculation (Lipinski Ro5 + Veber)
Read this after the foundation, then connect it to the previous step.
- 063 — Drug Interaction & Safety Lookup (OpenFDA)
Read this after the foundation, then connect it to the previous step.
- 074 — PubChem Compound Search
Read this after the foundation, then connect it to the previous step.
- 085 — Target & Disease Literature (OpenTargets)
Read this after the foundation, then connect it to the previous step.
- 09Reasoning Guidelines
Read this after the foundation, then connect it to the previous step.
- 10Important Notes
Finish here to verify the result and special cases.
Copy only after you understand the effect.
# Search compounds by target name (e.g. "EGFR", "COX-2", "ACE")
TARGET="$1"
ENCODED=$(python3 -c "import urllib.parse,sys; print(urllib.parse.quote(sys.argv[1]))" "$TARGET")
curl -s "https://www.ebi.ac.uk/chembl/api/data/target/search?q=${ENCODED}&format=json" \
| python3 -c "
import json,sys
data=json.load(sys.stdin)
targets=data.get('targets',[])[:5]
for t in targets:
print(f\"ChEMBL ID : {t.get('target_chembl_id')}\")
print(f\"Name : {t.get('pref_name')}\")
print(f\"Type : {t.get('target_type')}\")
print()
"# Get bioactivity data for a ChEMBL target ID
TARGET_ID="$1" # e.g. CHEMBL203
curl -s "https://www.ebi.ac.uk/chembl/api/data/activity?target_chembl_id=${TARGET_ID}&pchembl_value__gte=6&limit=10&format=json" \
| python3 -c "
import json,sys
data=json.load(sys.stdin)
acts=data.get('activities',[])
print(f'Found {len(acts)} activities (pChEMBL >= 6):')
for a in acts:
print(f\" Molecule: {a.get('molecule_chembl_id')} | {a.get('standard_type')}: {a.get('standard_value')} {a.get('standard_units')} | pChEMBL: {a.get('pchembl_value')}\")
"# Look up a specific molecule by ChEMBL ID
MOL_ID="$1" # e.g. CHEMBL25 (aspirin)
curl -s "https://www.ebi.ac.uk/chembl/api/data/molecule/${MOL_ID}?format=json" \
| python3 -c "
import json,sys
m=json.load(sys.stdin)
props=m.get('molecule_properties',{}) or {}
print(f\"Name : {m.get('pref_name','N/A')}\")
print(f\"SMILES : {m.get('molecule_structures',{}).get('canonical_smiles','N/A') if m.get('molecule_structures') else 'N/A'}\")
print(f\"MW : {props.get('full_mwt','N/A')} Da\")
print(f\"LogP : {props.get('alogp','N/A')}\")
print(f\"HBD : {props.get('hbd','N/Read the first command and identify its inputs and outputs before copying it.
Match every command to your installed Hermes version, review the files and accounts it can reach, and use non-sensitive data for the first test. If this explanation differs from the source, the official source wins.