About Us
The physicochemical properties and binding modes of protein-ligand complexes are crucial for studying protein functions, predicting protein binding pockets, screening small molecule ligands, and designing drugs. To this end, we have created CpuPDB
CpuPDB is a comprehensive 3D database of protein-ligand binding sites and cavities. CpuPDB aims to provide detailed information on protein-ligand binding cavities, binding sites, and interaction forces by processing data from the Protein Data Bank (PDB)
CpuPDB includes
- 37,864 PDB files and 17,193 biologically relevant ligands
- 67978 protein pockets and binding sites
- 2352 DynamicPockets
- interaction force calculation data for 89477 cavities and 102183 binding sites
- eight distinct interaction types including hydrogen bonds and salt bridges at each binding site
- detailed annotations of the physicochemical properties of proteins and their ligands
- An informative EXPLORE page for investigating protein families
- Protein dynamics data is used to discover cryptic protein pockets and key binding sites
CpuPDB can significantly advance the fields of structural biology and drug discovery
Services
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- Contact us：cpupdb@gmail.com if you can't find what you need
PdbID 4-character PDB identifier or partial like. Example: 11GS, 1A2B, 1G, GS. This is the unique code for each protein structure in the Protein Data Bank.
LigandID 3-character ligand code or partial like. Example: GSH, ATP, NAD, 2G, SH. These are standard identifiers for small molecules that bind to proteins.
LigSmiles SMILES string for chemical structure. Example: OS(CCN1CCOCC1)(O)O. This is a text representation of molecular structure.
ProteinSequence Amino acid sequence in FASTA format. Enter the protein sequence to find similar structures in our database.
DynamicsData Search for molecular dynamics simulation data. Example: 12AS. This helps identify conformational changes and cryptic pockets.
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Contact
Please contact us through the following way, welcome your visit
Our Address
639 Longmian Avenue, Jiangning District, Nanjing City, Jiangsu Province
Email Us
liaojun@cpu.edu.cn
Call Us
+86 025-86185160