Does this skill require a separate server deployment?

No, the pdb skill runs locally by making direct HTTP requests to the RCSB PDB web API, requiring no external infrastructure like Modal.

What file formats are supported for protein structures?

The skill supports fetching structures in both the traditional PDB (.pdb) format and the modern mmCIF (.cif) format, as well as FASTA sequences.

How does this skill assist in binder design?

It automates target preparation tasks such as removing water/ligands, trimming the structure to a binding region, and identifying potential hotspots for docking.

Can I search for proteins using an amino acid sequence?

Yes, the skill provides patterns for sequence-based searches through the RCSB Search API, allowing you to specify identity and e-value cutoffs.

RCSB PDB Structure Manager

Name: RCSB PDB Structure Manager
Author: adaptyvbio

byadaptyvbio

•

Ciencia de Datos y ML

Fetches, analyzes, and prepares protein structures from the RCSB Protein Data Bank for computational biology workflows.

The pdb skill empowers Claude to interact directly with the RCSB Protein Data Bank, facilitating the retrieval of high-resolution protein structures and metadata. It streamlines the complex process of target preparation for protein design by providing automated patterns for chain extraction, structural trimming, and interface residue identification. Whether you are searching for homologous structures via sequence similarity or preparing a specific binding site for de novo design, this skill provides the essential tools to handle structural data efficiently within your development environment.

Características Principales

01Advanced search by sequence similarity, E-value cutoffs, and full-text queries

0275 GitHub stars

03Direct retrieval of PDB and mmCIF structure files via RCSB APIs

04Automated chain extraction and structural preparation using BioPython

05Interface analysis tools to identify interacting residues and hotspots

06Structure trimming and renumbering for focused binder design tasks

Casos de Uso

01Preparing target proteins for binder design workflows by trimming to specific binding regions

02Automating the download and cleaning of protein datasets for machine learning models

03Analyzing protein-protein interfaces to identify critical residues for mutagenesis studies

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add adaptyvbio/protein-design-skills pdb

For use in Claude.ai and ChatGPT

Download Skill