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protein-structure-visualizer

Visualize and analyze protein structures from PDB IDs, AlphaFold entries, or local files.

64|12|Updated Apr 7, 2026
Search Tags:#visualization#pdb#alphafold#protein-structure#ppi#secondary-structure#pocket-detection
One-click install
npx skills add https://github.com/MDhewei/bioinfor-claw --skill protein-structure-visualizer
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: protein-structure-visualizer
Source: https://github.com/MDhewei/bioinfor-claw/tree/main/protein-structure-analysis/protein-structure-visualizer
Command: npx skills add https://github.com/MDhewei/bioinfor-claw --skill protein-structure-visualizer

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

Visualize and analyze protein structures from PDB IDs, AlphaFold UniProt entries, or local PDB files.

Core Features & Use Cases

  • Interactive 3D structure visualization via an HTML viewer (py3Dmol) for full proteins or specific chains/residues.
  • Per-residue analyses including Cα coordinates, B-factors / pLDDT, secondary structure timelines, SASA-based pocket detection, and conservation coloring.
  • Protein-Protein Interaction (STRING) networks and integration of structural data to contextualize function; applicable to comparative studies and drug-target exploration.

Quick Start

Run a full analysis on PDB 1TUP and generate the interactive viewer, pocket results, and conservation data in the specified output directory.

Frequently Asked Questions about protein-structure-visualizer

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

FAQPage Schema
How do I visualize a protein structure from a PDB ID?▼

To visualize a protein structure from a PDB ID, you can use an interactive 3D viewer like py3Dmol. This tool fetches structural data directly from PDB entries and generates an interactive HTML viewer, allowing you to explore full proteins, specific chains, or individual residues.

Can I analyze AlphaFold structures and extract pLDDT scores?▼

Yes, you can analyze AlphaFold structures by inputting UniProt entries. The analysis extracts per-residue data including Cα coordinates and pLDDT scores, outputting the results as visual plots and TSV data files for downstream evaluation.

How do I detect binding pockets in a protein using SASA?▼

Pocket detection is performed using Solvent Accessible Surface Area (SASA) analysis. By calculating per-residue SASA values, the tool identifies potential binding pockets and outputs pocket surface visualizations to a specified directory for drug-target exploration.

Does this protein structure analysis workflow support Protein-Protein Interaction networks?▼

Yes, the workflow supports Protein-Protein Interaction (PPI) networks. It integrates STRING network data with structural information to contextualize protein function, outputting network plots that are applicable for comparative studies and drug-target exploration.

What output formats are generated for protein structure analysis?▼

The analysis generates an interactive HTML viewer for 3D visualization, graphical plots in PNG and PDF formats for secondary structure timelines, TSV files for per-residue data, and dedicated pocket surface pages.

Do I need local PDB files to run secondary structure analysis?▼

No, you do not need local PDB files. The tool accepts PDB IDs and AlphaFold UniProt entries to fetch data remotely, but it also fully supports processing local PDB files if you have them available on your system.

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