Learn to effectively use tools for deposition, searching, analysis, and visualization of PDB data. Guide to PDB Data. Guided reference for exploration and interpretation of PDB entries. Molecule of the Month. Accounts of selected molecules from the PDB. Educational Resources. Resources promoting exploration in the world of proteins and nucleic ...

2024年10月5日 · These identifiers are used to specifically select, visualize, locate a specific instance of a ligand, amino acid in a protein chain in a particular PDB entry. Hence learning about them can help specifically locate, visualize, and analyze all or specific parts of PDB structures.

2023年4月10日 · PDBsum is a pictorial database that provides an at-a-glance overview of the contents of each 3D structure deposited in the Protein Data Bank (PDB). It shows the molecule (s) that make up the structure (ie protein chains, DNA, ligands and metal ions) and schematic diagrams of the interactions between them.

As a member of the wwPDB, the RCSB PDB curates and annotates PDB data according to agreed upon standards. The RCSB PDB also provides a variety of tools and resources. Users can perform simple and advanced searches based on annotations relating to …

The RCSB PDB offers two ways to access data through application programming interfaces (APIs): Stay current with API announcements by subscribing to the RCSB PDB API mailing list: The REST-based API supports the HTTP GET method to access the PDB data through a set of endpoints (or URLs).

The Protein Data Bank (PDB) [1] is a database for the three-dimensional structural data of large biological molecules such as proteins and nucleic acids, which is overseen by the Worldwide Protein Data Bank (wwPDB).

A typical PDB entry will contain atomic coordinates for a diverse collection of proteins, small molecules, ions and water.

What information does a PDB entry contain? Is the protein an enzyme? What specific biological processes are associated with the proteins? Which sequence family does the protein belong to? What protein signatures can be found in the structure? What are the structural folds/domains present in the proteins from this entry?

A typical PDB entry consists of the 3D coordinates of proteins and/or nucleic acids (e.g. DNA, RNA) along with bound molecules (e.g. sugars, lipids, inhibitors, metals etc.) and solvent (e.g. water) molecules. Each PDB entry is an experimentally-determined macromolecular structure.

The PDB file format is the standard file format for protein structure files. It describes how molecules are held together in 3-D structure of a protein. The file contains hundreds or thousands of lines called record, which describes about protein.