text-based-molecule-editing

Name: text-based-molecule-editing
Availability: InStock
Author: PharMolix

Edit molecular structures from natural language prompts using MolT5/BioT5 pipelines.

1.1k|132|Updated Apr 13, 2023

Search Tags:#drug-discovery #smiles #text-based #molecular-design #molecule-editing #bioT5 #molT5

Ready to run

npx skills add https://github.com/PharMolix/OpenBioMed --skill text-based-molecule-editing

💬 Prompt for ChatGPT / Claude Chat▼

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

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

Edit molecular structures based on natural language prompts to optimize properties, enabling rapid exploration of design space and reducing manual SMILES tweaking.

Core Features & Use Cases

Property-guided edits to improve solubility, potency, and pharmacokinetic profiles.
Scaffold modification and generation of molecular variants guided by textual prompts.
End-to-end design workflows using MolT5/BioT5 models and editable pipelines.

Quick Start

Provide a molecule input (SMILES or name) and a natural language edit prompt to receive an edited molecule.

Frequently Asked Questions about text-based-molecule-editing

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

FAQPage Schema

How do I edit molecular structures using natural language prompts?▼

To edit molecular structures using natural language prompts, provide a molecule input as a SMILES string or name along with a textual instruction to receive an edited molecule optimized for desired properties.

Can I optimize drug properties like solubility without manual SMILES tweaking?▼

Yes, you can optimize drug properties like solubility without manual SMILES tweaking by using property-guided text-driven edits to rapidly explore the molecular design space.

How do I perform scaffold modifications and generate molecular variants?▼

Perform scaffold modifications and generate molecular variants by inputting a base molecule and using text prompts to guide the structural edits for generating specific molecular alternatives.

Do I need MolT5 or BioT5 checkpoints for text-based molecule editing?▼

Yes, text-based molecule editing requires MolT5 or BioT5 pipelines and their associated checkpoints to process the input molecule and execute the natural language edit instructions.

What metrics are used to evaluate edited molecules?▼

Edited molecules are evaluated using QED, LogP, and SA metrics to measure the quantitative estimate of drug-likeness, lipophilicity, and synthetic accessibility of the generated structures.

When should I use text-based molecule editing instead of manual molecular design?▼

Use text-based molecule editing instead of manual molecular design when you need to rapidly explore design space, optimize pharmacokinetic profiles, or execute scaffold modifications guided by natural language.