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The Protein Data Bank (PDB) file format is a textual file format describing the three-dimensional structures of molecules held in the Protein Data Bank, now succeeded by the mmCIF format. The PDB format accordingly provides for description and annotation of protein and nucleic acid structures including atomic coordinates, secondary structure ...
The Bio.PDB module can load molecular structures from PDB and mmCIF files, and was added to Biopython in 2003. [16] The Structure object is central to this module, and it organises macromolecular structure in a hierarchical fashion: Structure objects contain Model objects which contain Chain objects which contain Residue objects which contain ...
162,041 structures in the PDB have a structure factor file. 11,242 structures have an NMR restraint file. 5,774 structures in the PDB have a chemical shifts file. 13,388 structures in the PDB have a 3DEM map file deposited in EM Data Bank. Most structures are determined by X-ray diffraction, but about 7% of structures are determined by protein ...
Download QR code; Print/export ... Template documentation ... This template provides a simple link to the Protein Data Bank and be used for up to 9 PDB accessions ...
The PDBbind database is a comprehensive collection of experimentally measured binding affinity data (Kd, Ki, and IC50) for the protein-ligand complexes deposited in the Protein Data Bank (PDB). [ 1 ] [ 2 ] It thus provides a link between energetic and structural information of protein-ligand complexes, which is of great value to various studies ...
The wwPDB maintained the specifications of the PDB file format and its XML alternative, PDBML. There was a fairly major change in PDB format specification (to version 3.0) in August 2007, and a remediation of many file problems in the existing database. [3] The typical file extension for a PDB file was .pdb, although some older files used .ent ...
The wwPDB was founded in 2003 by RCSB PDB (USA), PDBe (Europe) and PDBj (Japan). In 2006 BMRB (USA) joined the wwPDB. EMDB (UK) joined in 2021. Each member's site can accept structural data and process the data. The processed data is sent to the "archive keeper". The RCSB PDB presently acts as the "archive keeper".
BindingDB's web-interface provides a range of browsing, query and data download tools. These include browsing by the name of a protein Target or by journal citation, query by chemical similarity and substructure, and downloads by target or query result.