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MDhewei
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Protein Structure Alignment

Align two protein structures by Cα superimposition to compute global RMSD and per-residue deviations.

64|12|Updated Apr 7, 2026
Search Tags:#structure#AlphaFold#PDB#alignment#biopython#protein#RMSD
One-click install
npx skills add https://github.com/MDhewei/bioinfor-claw --skill protein-structure-alignment
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: Protein Structure Alignment
Source: https://github.com/MDhewei/bioinfor-claw/tree/main/protein-structure-analysis/protein-structure-alignment
Command: npx skills add https://github.com/MDhewei/bioinfor-claw --skill protein-structure-alignment

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires biopython, matplotlib, numpy, pandas, requests, py3Dmol, and includes scripts (resource) components.

What problem does it solve?

Protein structure comparison often requires manual, time-consuming structural alignment to quantify similarity and identify divergent regions. This Skill automates alignment and analysis of two structures by Cα atom superimposition, producing RMSD metrics and visualizations.

Core Features & Use Cases

  • Global and per-residue RMSD calculation after alignment.
  • Automated retrieval of structures from PDB, AlphaFold, or local files.
  • Interactive 3D viewer and publication-ready outputs for reports.
  • Use Cases: compare wild-type vs mutant structures; apo vs holo conformations; assess structural conservation across homologs.

Quick Start

Run the alignment on two PDB structures by providing their IDs through the CLI, e.g., python scripts/protein_structure_alignment.py --pdb1 1AKE --pdb2 4AKE --outdir results/.

Frequently Asked Questions about Protein Structure Alignment

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

FAQPage Schema
How do I calculate RMSD between two protein structures from PDB files?▼

To calculate RMSD between protein structures, this Skill aligns two structures via Cα superimposition using Biopython's Superimposer, outputting global RMSD and per-residue deviation metrics as summary TSVs.

Can I compare AlphaFold models with PDB structures using Biopython?▼

Yes, you can compare AlphaFold models with PDB structures. The Skill retrieves structures from PDB, AlphaFold, or local files, pairs Cα atoms by chain and residue sequence, and computes structural alignment RMSD.

How do I align wild-type vs mutant protein structures to find divergent regions?▼

Aligning wild-type vs mutant structures requires Cα superimposition to compute global and per-residue deviations. This Skill automates the alignment and identifies structurally divergent regions across the compared proteins.

Does Biopython support 3D visualization of protein structure alignment results?▼

Biopython computes the alignment, while py3Dmol handles 3D visualization of protein structure alignment results. The Skill generates an interactive HTML viewer to visually inspect the superimposed structures.

What's the best way to assess structural conservation across homologous proteins?▼

Assessing structural conservation across homologs is done by Cα superimposition to compute RMSD. This Skill automates the process, handling inputs from PDB or AlphaFold to quantify structural similarity.

Do I need pandas and NumPy to compute per-residue RMSD deviations?▼

Yes, you need pandas and NumPy installed. The Skill depends on these libraries alongside Biopython to process structural data and output per-residue deviation metrics into summary TSV files.

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