What can I do with the PDB Database skill?

You can search for protein and nucleic acid structures, retrieve detailed metadata like resolution or experimental methods, and download 3D coordinate files for structural analysis.

Can I search for proteins using amino acid sequences?

Yes, the skill supports sequence similarity searches with customizable identity and e-value cutoffs to find related structures in the RCSB database.

Which file formats does this skill support for downloads?

It supports the modern mmCIF standard, legacy PDB formats, and BinaryCIF for efficient data handling and high-resolution structural modeling.

Is this skill suitable for drug discovery?

Absolutely. It is designed to help identify binding pockets, compare protein-ligand complexes, and automate data retrieval for virtual screening and computational docking.

PDB Structural Biology & Drug Discovery

Name: PDB Structural Biology & Drug Discovery
Author: K-Dense-AI

byK-Dense-AI

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3,719

Data Science & ML

Accesses and analyzes RCSB Protein Data Bank (PDB) structures, metadata, and 3D coordinates for structural biology and drug discovery research.

About

The PDB Database skill enables Claude to interact directly with the RCSB Protein Data Bank, the global repository for 3D biological macromolecular structures. It provides comprehensive capabilities for searching protein and nucleic acid structures via text, sequence identity, or structural similarity, while also facilitating the retrieval of high-resolution metadata and experimental coordinates in formats like PDB and mmCIF. This tool is essential for researchers and developers performing computational drug discovery, protein engineering, or complex bioinformatics workflows requiring precise structural data from over 200,000 entries.

Key Features

Batch processing of multiple PDB entries for large-scale comparative analysis.
Advanced structure search by text, organism, resolution, and experimental method.
Automated downloading of coordinate files in PDB, mmCIF, and BinaryCIF formats.
3,719 GitHub stars
Retrieval of detailed structural metadata using flexible GraphQL queries.
Sequence and structural similarity queries across 200,000+ entries.

Use Cases

Identifying drug targets and analyzing ligand binding sites for pharmaceutical research.
Finding homologous structures to assist in protein folding and engineering tasks.
Automating the collection of experimental quality metrics for structural biology datasets.

About

Key Features

Batch processing of multiple PDB entries for large-scale comparative analysis.
Advanced structure search by text, organism, resolution, and experimental method.
Automated downloading of coordinate files in PDB, mmCIF, and BinaryCIF formats.
3,719 GitHub stars
Retrieval of detailed structural metadata using flexible GraphQL queries.
Sequence and structural similarity queries across 200,000+ entries.

Use Cases

Identifying drug targets and analyzing ligand binding sites for pharmaceutical research.
Finding homologous structures to assist in protein folding and engineering tasks.
Automating the collection of experimental quality metrics for structural biology datasets.