The Protein Data Bank

About

Quote

Since 1971, the Protein Data Bank archive (PDB) has served as the single repository of information about the 3D structures of proteins, nucleic acids, and complex assemblies.

• PDB Website
• PDB Ligand Downloads
• PDB Archives

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About this App

Simmate's pdb app helps to download PDB data & load it into the Simmate database.

Module	CLI	Workflows	Data
simmate.apps.pdb

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Installation

1. Add pdb to the list of installed Simmate apps with:

   simmate config add pdb
   

2. Ensure everything is configured correctly:

   simmate config test pdb
   

3. Add new tables to your database:

   simmate database update
   

4. Download all PDB datasets:

   simmate database download pdb
   

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Datasets

Dataset	Disk Space	Rows (#)	SQL Table	Python Class
Ligand Molecules	---	---	pdb__ligands	PdbLigand

Tip

Read through our database guide to learn how to work with these datasets

Example

python

from simmate.database import connect
from simmate.apps.pdb.models import PdbLigand

mol_sample_data = PdbLigand.objects.to_dataframe(limit=5_000)

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