ReddRadar
Agent skill
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.
Install this agent skill to your Project
npx add-skill https://github.com/adaptyvbio/protein-design-skills/tree/main/skills/pdb
SKILL.md
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
# 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
from Bio.PDB import PDBList
pdbl = PDBList()
pdbl.retrieve_pdb_file("1ABC", pdir="structures/", file_format="pdb")
Using RCSB API
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
from Bio.PDB import PDBParser, PDBIO, Select
class ChainSelect(Select):
def __init__(self, chain_id):
self.chain_id = chain_id
def accept_chain(self, chain):
return chain.id == self.chain_id
# Extract chain A
parser = PDBParser()
structure = parser.get_structure("protein", "1abc.pdb")
io = PDBIO()
io.set_structure(structure)
io.save("chain_A.pdb", ChainSelect("A"))
Trimming to Binding Region
def trim_around_residues(pdb_file, center_residues, buffer=10.0):
"""Trim structure to region around specified residues."""
parser = PDBParser()
structure = parser.get_structure("protein", pdb_file)
# Get center coordinates
center_coords = []
for res in structure.get_residues():
if res.id[1] in center_residues:
center_coords.extend([a.coord for a in res.get_atoms()])
center = np.mean(center_coords, axis=0)
# Keep residues within buffer
class RegionSelect(Select):
def accept_residue(self, res):
for atom in res.get_atoms():
if np.linalg.norm(atom.coord - center) < buffer:
return True
return False
io = PDBIO()
io.set_structure(structure)
io.save("trimmed.pdb", RegionSelect())
Searching PDB
RCSB Search API
import requests
query = {
"query": {
"type": "terminal",
"service": "full_text",
"parameters": {
"value": "EGFR kinase domain"
}
},
"return_type": "entry"
}
response = requests.post(
"https://search.rcsb.org/rcsbsearch/v2/query",
json=query
)
results = response.json()
By Sequence Similarity
query = {
"query": {
"type": "terminal",
"service": "sequence",
"parameters": {
"value": "MKTAYIAKQRQISFVK...",
"evalue_cutoff": 1e-10,
"identity_cutoff": 0.9
}
}
}
Structure Analysis
Get Chain Info
def get_structure_info(pdb_file):
parser = PDBParser(QUIET=True)
structure = parser.get_structure("protein", pdb_file)
info = {
"chains": [],
"total_residues": 0
}
for model in structure:
for chain in model:
residues = list(chain.get_residues())
info["chains"].append({
"id": chain.id,
"length": len(residues),
"first_res": residues[0].id[1],
"last_res": residues[-1].id[1]
})
info["total_residues"] += len(residues)
return info
Find Interface Residues
def find_interface_residues(pdb_file, chain_a, chain_b, distance=4.0):
"""Find residues at interface between two chains."""
parser = PDBParser(QUIET=True)
structure = parser.get_structure("complex", pdb_file)
interface_a = set()
interface_b = set()
for res_a in structure[0][chain_a].get_residues():
for res_b in structure[0][chain_b].get_residues():
for atom_a in res_a.get_atoms():
for atom_b in res_b.get_atoms():
if atom_a - atom_b < distance:
interface_a.add(res_a.id[1])
interface_b.add(res_b.id[1])
return interface_a, interface_b
Common Tasks for Binder Design
Target Preparation Checklist
- Download structure:
curl -o target.pdb "https://files.rcsb.org/download/XXXX.pdb" - Identify target chain
- Remove waters and ligands (if needed)
- Trim to binding region + buffer
- Identify potential hotspots
- Renumber if needed
Troubleshooting
Structure not found: Check PDB ID format (4 characters) Multiple models: Select first model for design Missing residues: Check for gaps in structure
Next: Use structure with boltzgen (recommended) or rfdiffusion for design.
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