pgdh_rfdiffusion3

Name: pgdh_rfdiffusion3
Availability: InStock
Author: Alex

Generate atomic-level protein binders for 15-PGDH using RFdiffusion3 on Lyceum.

Updated Feb 27, 2026

Search Tags:#protein design #binder design #RFdiffusion3 #computational biology #Lyceum #15-PGDH

Ready to run

npx skills add https://github.com/alex-hh/in-silico-pgdh --skill pgdh-rfdiffusion3

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: pgdh_rfdiffusion3
Source: https://github.com/alex-hh/in-silico-pgdh/tree/main/.claude/skills/pgdh_rfdiffusion3
Command: npx skills add https://github.com/alex-hh/in-silico-pgdh --skill pgdh-rfdiffusion3

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill automates the generation of atomic-level protein binders targeting the 15-PGDH enzyme using the advanced RFdiffusion3 tool.

Core Features & Use Cases

Atomic-level Design: Generates full sidechain placements for binders, not just backbones.
Targeted Binding: Supports designing binders for specific sites like the active site or dimer interface of 15-PGDH.
Use Case: Generate novel protein binders that can block the active site of 15-PGDH to inhibit its function, using a specified set of hotspot residues.

Quick Start

Use the pgdh_rfdiffusion3 skill to generate 4 PGDH active site binder designs using the rosettacommons/foundry Docker image on Lyceum.

Frequently Asked Questions about pgdh_rfdiffusion3

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

FAQPage Schema

How do I design protein binders for the 15-PGDH enzyme using RFdiffusion3?▼

To design protein binders for 15-PGDH, you can use this Skill to run RFdiffusion3 on the Lyceum platform, generating atomic-level binders with full sidechain placements. It requires specifying target sites and hotspot residues via a JSON configuration.

Can I target specific sites like the active site or dimer interface when designing PGDH binders?▼

Yes, you can target specific sites such as the active site or dimer interface of 15-PGDH. The Skill uses precise hotspot residue specification to generate novel protein binders that can effectively block the enzyme's function at these designated locations.

Does protein binder generation with RFdiffusion3 require a specific Docker environment?▼

Yes, protein binder generation with RFdiffusion3 requires the rosettacommons/foundry Docker image for execution on the Lyceum platform. This environment provides the necessary computational biology framework to process the JSON configuration and generate designs.

What is the difference between atomic-level protein design and backbone-only generation for binders?▼

Atomic-level protein design generates full sidechain placements for binders rather than just backbones. This approach ensures complete structural detailing of the designed protein binders targeting the 15-PGDH enzyme using the RFdiffusion3 tool.

How do I configure hotspot residues for computational binder design?▼

You configure hotspot residues for computational binder design by defining them within a JSON configuration file. This precise specification is required to direct RFdiffusion3 to generate binders targeting specific functional sites on the 15-PGDH enzyme.

What are the limitations of using RFdiffusion3 for PGDH binder design?▼

A key limitation of using RFdiffusion3 for PGDH binder design is the strict requirement for precise hotspot specification. The tool cannot effectively generate targeted binders without accurate hotspot residue configuration provided in the JSON input.