pdb
Fetch and analyze protein structures from RCSB PDB. Use this skill when: (1) Need to download a structure by PDB ID, (2) Search for similar structures, (3) Prepare target for binder design, (4) Extract specific chains or domains, (5) Get structure metadata. For sequence lookup, use uniprot. For binder design workflow, use binder-design.
npx skills add majiayu000/claude-skill-registry --skill pdb-adaptyvbio-protein-design-skill-2 --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# PDB Database Access **Note**: This skill uses the RCSB PDB web API directly. No Modal deployment needed - all operations run locally via HTTP requests. ## Fetching Structures ### By PDB ID ```bash # Download PDB file curl -o 1alu.pdb "https://files.rcsb.org/download/1ALU.pdb" # Download mmCIF curl -o 1alu.cif "https://files.rcsb.org/download/1ALU.cif" ``` ### Using Python ```python from Bio.PDB import PDBList pdbl = PDBList() pdbl.retrieve_pdb_file("1ABC", pdir="structures/", file_format="pdb") ``` ### Using RCSB API ```python import requests def fetch_pdb(pdb_id: str, format: str = "pdb") -> str: """Fetch structure from RCSB PDB.""" url = f"https://files.rcsb.org/download/{pdb_id}.{format}" response = requests.get(url) response.raise_for_status() return response.text def fetch_fasta(pdb_id: str) -> str: """Fetch sequence in FASTA format.""" url = f"https://www.rcsb.org/fasta/entry/{pdb_id}" return requests.get(url).text # Example usage pdb_content = fetch_pdb("1ALU") with open("1ALU.pdb", "w") as f: f.write(pdb_content) ``` ## Structure Preparation ### Selecting Chains ```python from Bio.PDB import PDBParser, PDBIO, Select class ChainSelect(Select): def __init__(self, chain_id):
- Fetching Structures
- By PDB ID
- Using Python
- Using RCSB API
- Structure Preparation
- Selecting Chains
- Trimming to Binding Region
- Searching PDB
- RCSB Search API
- By Sequence Similarity
- Structure Analysis
- Get Chain Info
- Find Interface Residues
- Common Tasks for Binder Design
Download PDB file curl -o 1alu.pdb "https://files.rcsb.org/download/1ALU.pdb" Download mmCIF curl -o 1alu.cif "https://files.rcsb.org/download/1ALU.cif"
What does the pdb skill do?
Fetch and analyze protein structures from RCSB PDB. Use this skill when: (1) Need to download a structure by PDB ID, (2) Search for similar structures, (3) Prepare target for binder design, (4) Extract specific chains or domains, (5) Get structure metadata. For sequence lookup, use uniprot. For binder design workflow, use binder-design.
How do I install it?
Run `npx skills add majiayu000/claude-skill-registry --skill pdb-adaptyvbio-protein-design-skill-2 --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From majiayu000/claude-skill-registry, a repository with 534 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.