Description
medchem is an agent skill for medicinal chemistry compound triage with the medchem Python library from datamol-io. It applies drug-likeness rules, such as Lipinski, Veber, CNS and lead-like rules, and structural alert catalogues, such as PAINS, NIBR and ChEMBL alerts. It also checks complexity thresholds against ZINC-derived values, detects functional groups and named substructure catalogues, and builds multi-criteria filters with a custom query language. Use it to triage compound libraries at scale, to prioritise compounds for hit-to-lead or lead optimisation work, or to filter molecules by structural alerts. The skill is clear that filters are context-specific guidelines, so their results should be combined with domain expertise and target knowledge rather than read as verdicts. The verified runtime is medchem 2.1.1, datamol 0.13.0 and RDKit 2026.3.6 on Python 3.11 or newer. The RuleFilters and structural classes return pandas DataFrames. Filters run locally, while installation and documentation lookups need a network connection. The Lilly native execution was not tested in that review.…
Highlights
- Lipinski, Veber, CNS and lead-like rules
- PAINS, NIBR and ChEMBL structural alerts
- Complexity thresholds
- Multi-criteria query language
- Results as pandas DataFrames
Ratings & Reviews
No ratings yet
Be the first to rate medchem.
People also visit
datamol
Pythonic wrapper around RDKit with simplified interface and sensible defaults
medchem FAQ
What does medchem do?
Applies medicinal chemistry filters to compound libraries, for triage and prioritisation.
Which rules and alerts?
Drug-likeness rules such as Lipinski, Veber, CNS and lead-like, and alert catalogues such as PAINS, NIBR and ChEMBL.
Should I trust a filter's verdict?
The skill says filters are context-specific guidelines and should be combined with domain expertise and target knowledge.
What does it run on?
medchem 2.1.1, datamol 0.13.0 and RDKit 2026.3.6 on Python 3.11 or newer. Filters run locally.
How do I install it?
Run npx skills add https://github.com/k-dense-ai/scientific-agent-skills --skill medchem.
Is it checked for security?
Its security audits show passes from Gen Agent Trust Hub, Socket and Snyk.
What are the best medchem alternatives?
Popular alternatives to medchem include datamol, rdkit and deepchem. See all medchem alternatives