bio-covalent-design
Designs covalent inhibitors and warheads targeting cysteine (most common, 98% of covalent drugs), lysine, serine, threonine, tyrosine, and aspartate residues, with explicit handling of warhead reactivity (acrylamide, chloroacetamide, vinyl sulfone, sulfonyl fluoride, fluorosulfate, aldehyde, boronate, nitrile), reversibility (kinact/Ki, t_residence), glutathione (GSH) stability, intrinsic reactivity assays, and covalent docking (DOCKovalent, GOLD, HCovDock). Use when designing covalent inhibitors for targeted covalent inhibition (TCI), KRAS G12C-style approaches, or rationalizing covalent SAR.
npx skills add BioTender-max/awesome-bio-agent-skills --skill covalent-design --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: RDKit 2024.09+, OpenEye / AutoDock Vina 1.2+ (for covalent extensions), GOLD (commercial), DOCKovalent (web service), HCovDock 1.0+. Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show rdkit` then `help(rdkit.Chem)` to check signatures - CLI: check version output of each docking tool If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Covalent Inhibitor Design Design molecules that form covalent bonds with target protein residues. The "covalent revolution" (Lonsdale & Ward 2018) made TCIs (Targeted Covalent Inhibitors) clinically validated: KRAS G12C inhibitors (sotorasib, adagrasib), BTK inhibitors (ibrutinib), and EGFR inhibitors (osimertinib) are recent successes. Postdoc-grade covalent design requires balancing **intrinsic reactivity** (must form bond) vs **selectivity** (only the intended residue), **reversibility** (irreversible vs reversible covalent), and **drug-likeness** (warheads can hurt PK). For warhead substructure filtering (in non-covalent contexts), see
- Version Compatibility
- Reactive Residue Taxonomy
- Warhead Chemistry
- Decision Tree by Scenario
- Kinetics: kinact / Ki
- Intrinsic Reactivity Assays
- Covalent Docking Tools
- Example: KRAS G12C Inhibitor Design Workflow
- Reactivity Surrogates (computed without experiment)
- Per-Tool Failure Modes
- Wrong warhead for residue
- Excessive reactivity (off-target)
- Geometric mismatch
- Reversibility unintended
What does the bio-covalent-design skill do?
Designs covalent inhibitors and warheads targeting cysteine (most common, 98% of covalent drugs), lysine, serine, threonine, tyrosine, and aspartate residues, with explicit handling of warhead reactivity (acrylamide, chloroacetamide, vinyl sulfone, sulfonyl fluoride, fluorosulfate, aldehyde, boronate, nitrile), reversibility (kinact/Ki, t_residence), glutathione (GSH) stability, intrinsic reactivity assays, and covalent docking (DOCKovalent, GOLD, HCovDock). Use when designing covalent inhibitors for targeted covalent inhibition (TCI), KRAS G12C-style approaches, or rationalizing covalent SAR.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill covalent-design --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.