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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). These structural data are obtained and deposited by biologists and biochemists worldwide through the use of experimental ...
The PDB file format was invented in 1972 [2][3] as a human-readable file that would allow researchers to exchange the atomic coordinates in a given protein through a database system. Its fixed-column width format is limited to 80 or 140 [4] columns, which was based on the width of the computer punch cards that were previously used to exchange ...
Protein structure database. In biology, a protein structure database is a database that is modeled around the various experimentally determined protein structures. The aim of most protein structure databases is to organize and annotate the protein structures, providing the biological community access to the experimental data in a useful way.
PDBbind database. 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 ...
The Worldwide Protein Data Bank, wwPDB, is an organization that maintains the archive of macromolecular structure. Its mission is to maintain a single Protein Data Bank Archive of macromolecular structural data that is freely and publicly available to the global community. [ 1][ 2] The organization has five members: [ 3] Research Collaboratory ...
Structure validation concept: model of a protein (each ball is an atom), and magnified region with electron density data and 3 bright flags for problems. Macromolecular structure validation is the process of evaluating reliability for 3-dimensional atomic models of large biological molecules such as proteins and nucleic acids.
PDBsum. Overview of the structures contained within the Protein Data Bank. PDBsum is a database that provides an overview of the contents of each 3D macromolecular structure deposited in the Protein Data Bank (PDB). [1][2][3][4]
Swiss-model. Swiss-model (stylized as SWISS-MODEL) is a structural bioinformatics web-server dedicated to homology modeling of 3D protein structures. [1][2] As of 2024, homology modeling is the most accurate method to generate reliable three-dimensional protein structure models and is routinely used in many practical applications.