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by-database

Queries PDB, UniProt, and SAbDab via MCP servers to produce structured CSV outputs for target characterization and scaffold selection.

104|10|Updated Mar 23, 2026
Search Tags:#pdb#uniprot#batch-lookup#by-database#sabdab#antibody-scaffold#structure-metadata
One-click install
npx skills add https://github.com/001TMF/blatant-why --skill by-database
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: by-database
Source: https://github.com/001TMF/blatant-why/tree/main/templates/.claude/skills/by-database
Command: npx skills add https://github.com/001TMF/blatant-why --skill by-database

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires httpx, and includes scripts (resource) components.

What problem does it solve?

This skill consolidates multidisciplinary data from PDB, UniProt, and SAbDab by querying BY MCP database servers to enable fast target characterization, scaffold selection, and competitive analysis.

Core Features & Use Cases

  • Batch lookups across PDB/UniProt/SAbDab for a target to assemble a cohesive data dossier.
  • Retrieve structural metadata, domain annotations, and known antibody–antigen complexes to inform scaffold selection and competition analysis.
  • Cross-reference data from multiple sources to reconcile residue numbering, organism, and chain information for design workflows.

Quick Start

Run a batch lookup against your target list to produce a consolidated CSV report.

Frequently Asked Questions about by-database

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

FAQPage Schema
How do I batch query PDB and UniProt for target characterization data?▼

Batch querying PDB and UniProt for target characterization involves submitting a target list to retrieve structural metadata and domain annotations, which this skill consolidates into a structured CSV report via deterministic MCP database lookups.

Can I retrieve antibody scaffold options and epitope context from SAbDab?▼

Retrieving antibody scaffold options and epitope context from SAbDab is supported by querying known antibody-antigen complexes, allowing you to extract structural metadata for scaffold selection and competition analysis.

What's the best way to cross-reference structural data across PDB, UniProt, and SAbDab?▼

Cross-referencing structural data across PDB, UniProt, and SAbDab is best handled by running batch lookups against all three sources, reconciling residue numbering, organism, and chain information into a unified CSV output.

Does this batch lookup approach require specific dependencies to query biological databases?▼

This batch lookup approach requires the httpx dependency to execute queries against BY MCP database servers, returning structured CSV outputs suitable for downstream design workflows.

How to assemble a cohesive target dossier using structural metadata and domain annotations?▼

Assembling a cohesive target dossier using structural metadata involves querying multiple biological databases to gather and consolidate target characterization data, scaffold options, and antibody-epitope context into a single report.

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