How does it help with resource planning?

The skill includes a detailed compute requirement guide, estimating GPU types (A10G, T4, A100) and timeframes required for various design campaign scales.

Can I use this for de novo binder design?

Yes, this skill is specifically optimized for end-to-end binder design pipelines, covering everything from target preparation and hotspot selection to final candidate filtering.

Does it include specific quality control metrics?

Yes, it provides standardized thresholds for critical metrics such as pLDDT (>0.85), ipTM (>0.50), PAE_interface (<10), and scRMSD (<2.0A).

What tools are supported by this protein design workflow?

The workflow integrates major protein design tools including RFdiffusion and BindCraft for backbones, ProteinMPNN for sequence design, and AlphaFold/ColabFold for structure validation.

Protein Design Workflow

Name: Protein Design Workflow
Author: adaptyvbio

byadaptyvbio

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Data Science & ML

Orchestrates end-to-end protein design pipelines from target preparation to validated structure selection.

This skill provides comprehensive, step-by-step guidance for planning and executing computational protein design projects, specifically focusing on binder design workflows. It streamlines the integration of industry-standard tools like RFdiffusion, ProteinMPNN, and ColabFold, offering standardized patterns for backbone generation, sequence design, and high-throughput validation. Ideal for researchers and bio-engineers, it includes detailed resource planning, quality control thresholds (pLDDT, ipTM, PAE), and troubleshooting tips to ensure efficient use of GPU compute and high-quality design outputs.

Key Features

01Step-by-step binder design pipeline orchestration

02Standardized quality checkpoints for every design phase

0375 GitHub stars

04Integration guidance for RFdiffusion, BindCraft, and ProteinMPNN

05Structure validation and filtering using AlphaFold/ColabFold metrics

06Compute resource planning and timeline estimations for GPU tasks

Use Cases

01Planning and initializing a new de novo protein binder design project

02Setting up automated validation pipelines for large-scale protein libraries

03Optimizing GPU resource allocation and timelines for protein design campaigns

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add adaptyvbio/protein-design-skills protein-design-workflow

For use in Claude.ai and ChatGPT

Download Skill