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alphafold-structure-prediction

Predicts protein structures with AlphaFold 2/3 and Boltz-1 from sequence input.

6|2|Updated Jun 11, 2026
Search Tags:#pLDDT#AlphaFold#PAE#protein structure prediction#Boltz-1#MSA generation
One-click install
npx skills add https://github.com/pradyumnasagar/open-research-skills --skill alphafold-structure-prediction
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: alphafold-structure-prediction
Source: https://github.com/pradyumnasagar/open-research-skills/tree/main/skills/machine-learning-bio/alphafold-structure-prediction
Command: npx skills add https://github.com/pradyumnasagar/open-research-skills --skill alphafold-structure-prediction

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires alphafold3, boltz, mmseqs2, hhsuite, py3Dmol, and includes scripts (resource) and references (resource) and assets (resource) components.

What problem does it solve?

This Skill predicts protein structures using AlphaFold 2/3 and Boltz-1, helping researchers and scientists save time and resources in protein structure prediction.

Core Features & Use Cases

  • Protein Structure Prediction: Run AlphaFold 2/3 and Boltz-1 for accurate protein structure prediction.
  • MSA Generation: Generate Multiple Sequence Alignments with MMseqs2 or HHblits.
  • pLDDT and PAE Interpretation: Analyze the confidence of predicted structures using pLDDT and PAE scores.
  • Multimer Prediction: Predict multimeric protein structures for protein-protein interactions.
  • AFDB Querying: Query the AlphaFold Database for existing protein structures.
  • Use Case: A researcher needs to predict the structure of a new protein for a drug discovery project. They can use this Skill to generate the structure and analyze its confidence using pLDDT and PAE scores.

Quick Start

Run the alphafold-structure-prediction skill to predict the structure of a protein sequence.

Frequently Asked Questions about alphafold-structure-prediction

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

FAQPage Schema
How do I predict protein structures using AlphaFold 2/3 and Boltz-1?▼

You can predict protein structures by inputting protein sequences, generating Multiple Sequence Alignments (MSA), and running AlphaFold 2/3 or Boltz-1 models to output accurate structural predictions for research workflows.

How do I generate Multiple Sequence Alignments for protein structure prediction?▼

Generate Multiple Sequence Alignments (MSA) using MMseqs2 or HHblits to provide the evolutionary context required for accurate structure prediction with AlphaFold 2/3 and Boltz-1.

How do I analyze AlphaFold pLDDT and PAE confidence scores?▼

Analyze predicted structure confidence using pLDDT and PAE scores to evaluate local and global accuracy, which is critical for validating protein structures in drug discovery workflows.

Can I predict multimeric protein structures with Boltz-1 and AlphaFold 3?▼

Yes, you can predict multimeric protein structures to model protein-protein interactions using AlphaFold 2/3 and Boltz-1, enabling analysis of complex biological assemblies.

Do I need to install AlphaFold 3 and Boltz-1 to predict protein structures?▼

Yes, AlphaFold 2/3, Boltz-1, MMseqs2, HHblits, and py3Dmol are required dependencies to execute the MSA generation, structure prediction, and structural visualization processes.

How do I query the AlphaFold Database for existing protein structures?▼

Query the AlphaFold Database to retrieve existing protein structures, bypassing the de novo prediction process and saving computational resources when structures are already available.

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