Menu

Individual skill

denovo-design

De novo molecule generation for drug discovery. Scaffold-based analog enumeration, fragment growing/linking, structure-based design, multi-objective optimization, and drug-likeness filtering.

backend/cli/skills/chemistry/denovo-design/SKILL.md

Read pinned source

Source commit a08e0ad0ad3d6448123039ee4659163eb2e35d99

What was checked

Matches the observed repository HEAD
Yes
Scanner rules are current
Yes
Repository scan complete
No
Skill scan complete
No
Observed behavior
Network or broad shell
Last checked
Nov 2, 2026

These are observations at the recorded commit, not a guarantee of safety. Review the source before running it.

Install this skill

Choose an agent in your Stack or copy a command below. Commands fetch the pinned commit and copy only this skill directory. Existing destinations are refused. Copying a command does not install anything.

An install command is unavailable: current rules, complete repository and skill scans, an eligible behavior level and a permitted license are required.

Repository context

Repository stars (not skill ratings)
4,353
Repository last updated
Nov 6, 2026
License
Apache-2.0

Observed agent integration: No specific integration evidence. Standard SKILL.md installation does not imply verified compatibility.

Files and excerpt

File metadata and permitted, redacted excerpts come from the recorded scan. Source links are pinned to that commit.

Browse files
Read excerpt

# De Novo Molecule Design

## Overview

De novo design is the computational generation of novel molecular structures with desired properties, without starting from known active compounds. This skill provides a complete toolkit for generating drug candidates through multiple complementary strategies: scaffold-based analog enumeration, fragment-based design, structure-based design (SBDD), multi-objective optimization, and drug-likeness filtering.

All generation strategies produce molecules with computed physicochemical properties and similarity metrics, enabling rapid prioritization. The scripts are designed for CPU-first execution using RDKit as the core cheminformatics engine, with optional GPU acceleration noted where applicable.

## When to Use This Skill

Use this skill when you need to:

- **Explore chemical space** around a known lead compound by generating analogs with R-group enumeration, bioisosteric replacements, or random mutations
- **Design molecules from fragments** by growing, linking, or merging fragment hits from screening campaigns