BioSymphony Small Molecules

BioSymphony Small Molecules is an agent skill for choosing open and publicly documented tools in small-molecule design.

Use the skill with Claude Code, Codex, Symphony, or another agent harness to:

• generate synthesizable molecules and design analogs
• plan retrosynthesis and assess reactions, templates, and makeability
• choose protein-structure, docking, co-folding, and affinity methods
• choose QSAR, ADMET, selectivity, and pocket-conditioned methods
• check code, model weights, data, and base-model terms

Repository Features

Agent need	What this repository adds
Pick a starting method	Task routing in SKILL.md and the compact tool matrix
Avoid loading too much context	Focused reference files by workflow category
Compare tools quickly	Tool cards with task fit, license notes, weights, data, and status
Connect target work to synthesis	A two-layer loop from target scoring back to makeable molecules
Keep public demos small	A compact KRAS molecular-glue example with public inputs and summaries

Agent Flow

flowchart TD
    A["User task"] --> B["Open SKILL.md"]
    B --> C["Identify task category"]
    C --> D["Load one focused reference"]
    D --> E["Choose first tool path"]
    E --> F["Check code, weights, data, and base-model terms"]
    F --> G["Run or recommend the smallest suitable workflow"]
    G --> H["Record limits and next decision"]

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Design Loop

flowchart LR
    A["Target question"] --> B["Structure, docking, co-folding, affinity"]
    B --> C["QSAR, ADMET, selectivity"]
    C --> D["Candidate set"]
    D --> E["Synthesizable projection and analogs"]
    E --> F["Retrosynthesis and route checks"]
    F --> G["Makeable candidates"]
    G --> B
    F --> H["License and data review"]
    B --> H

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How to Use It

Open SKILL.md. The skill routes by task:

• generate makeable analogs of a hit
• project a molecule into synthesizable space
• plan or check a synthesis route
• dock a ligand or co-fold a protein-ligand complex
• estimate binding affinity with an ML or free-energy method
• build QSAR, ADMET, or off-target screens
• generate molecules into a binding pocket
• check a tool's license and data terms for product-facing work

The reference files are plain Markdown. They work as agent context and as human-readable notes.

For Claude Code-style skill discovery:

ln -s "$(pwd)" ~/.claude/skills/small-molecule-design-tools

The skill name is small-molecule-design-tools.

What Is Included

SKILL.md                         agent entry point and routing table
references/tool-matrix.md        compact index of tools by task
references/licensing-and-data.md code, weights, data, and base-model checklist
references/*.md                  focused tool cards by category
demos/kras-glue/                 compact public-data demo on PDB 9BG6
assets/readme-banner.png         selected README banner image
scripts/public_audit.py          public-release scan for local paths, secrets, and links

The tool matrix contains 152 indexed rows across 18 categories. Grouped entries and cross-references count as one row each.

Start Points

Start here	Use it for
references/tool-matrix.md	One table across all tool categories
references/licensing-and-data.md	Code, weights, data, and base-model terms
references/synthesizable-generation.md	Makeable molecule generation and analog design
references/retrosynthesis-planning.md	Multi-step synthesis planning
references/docking-and-cofolding.md	Docking, co-folding, pose, and affinity tools
references/binding-affinity-and-fep.md	OpenFE, OpenMM, MM-GBSA, and related methods
references/worked-example-kras-glue.md	Applying the layers to a public KRAS molecular-glue structure

Public Repository Boundary

This repository contains documentation, skill instructions, compact public-data examples, and small result summaries. It excludes model weights, vendor catalogs, non-public scientific data, raw service output, and large generated media.

Run the public-release check:

make release-check

This command compiles the public Python scripts, checks local Markdown links, and scans for local workstation paths, secrets, and oversized files.

License

The repository content uses the MIT License. Each upstream project sets its own terms. The reference cards track source code, model weights, data, and base models separately because one project can apply different terms to each layer.