retrosynthesis-planning

Name: retrosynthesis-planning
Availability: InStock
Author: PharMolix

Plan retrosynthetic routes for complex molecules using AND/OR tree search and vendor validation.

1.1k|132|Updated Apr 13, 2023

Search Tags:#automation #planning #ai-assisted #retrosynthesis #rdkit #chemoinformatics

Ready to run

npx skills add https://github.com/PharMolix/OpenBioMed --skill retrosynthesis-planning

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: retrosynthesis-planning
Source: https://github.com/PharMolix/OpenBioMed/tree/main/skills/retrosynthesis-planning
Command: npx skills add https://github.com/PharMolix/OpenBioMed --skill retrosynthesis-planning

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires rdkit, requests, aizynthfinder, and includes scripts (resource) and references (resource) and assets (resource) components.

What problem does it solve?

Automates the planning of retrosynthetic routes for complex molecules, combining expert oversight with automated disconnection tools to accelerate discovery and ensure feasibility.

Core Features & Use Cases

AND/OR tree search: manage AND (reactions) and OR (molecules) nodes to explore multiple pathways with backpropagation of solvable leaves.
Vendor-centric validation: integrates automated checks for commercial availability of building blocks to prune infeasible branches early.
Extensible workflow: supports RDKit-based checks, code-generated heuristics, and on-demand script execution to refine routes.
Use Case: In drug discovery, quickly generate synthetic routes for a new target and verify each fragment's purchasability before experimental work.

Quick Start

Provide a target molecule SMILES to begin, and I will initialize the planning workspace and start exploring retrosynthetic routes.

Frequently Asked Questions about retrosynthesis-planning

High-intent search queries and answers about installing and using this skill.

FAQPage Schema

How do I plan retrosynthetic routes for complex molecules using AI?▼

Retrosynthetic route planning combines expert judgment with automated disconnection tools to decompose a target molecule. You provide a target molecule SMILES, and the system initializes a workspace to explore pathways, validate building blocks, and generate a checkpointed tree.

Can I validate commercial availability of building blocks during retrosynthesis?▼

Yes, retrosynthetic planning includes vendor-centric validation to check commercial availability of building blocks. This automated integration prunes infeasible branches early, ensuring that generated pathways backpropagate to purchasable starting materials before experimental work begins.

How does AI-assisted disconnection manage multiple synthesis pathways?▼

AI-assisted disconnection manages multiple synthesis pathways using an AND/OR tree search. It handles AND nodes for reactions and OR nodes for molecules, allowing exploration of multiple routes with backpropagation of solvable leaves to identify feasible synthetic pathways.

Does retrosynthesis planning work with RDKit for molecule validation?▼

Retrosynthesis planning supports RDKit-based checks to validate molecules and refine routes within an extensible workflow. This integration allows users to apply chemoinformatics constraints and code-generated heuristics during the automated disconnection process.

What is the best way to automate retrosynthetic analysis for drug discovery?▼

Automating retrosynthetic analysis for drug discovery is best handled by a system combining expert-in-the-loop oversight with automated tools. This approach generates synthetic routes for new targets while verifying fragment purchasability and maintaining reproducible state management.

Do I need aizynthfinder to perform automated retrosynthetic planning?▼

Automated retrosynthetic planning utilizes aizynthfinder as a dependency to drive AI-based disconnection. Combined with requests and rdkit, this framework enables end-to-end workflow execution including molecule analysis, route exploration, and validation backpropagation.