Introduction to Protein Data Bank Format
Introduction to Protein Data Bank Format. Protein Data Bank (PDB) format is a standard for files containing atomic coordinates. It is used for structures in the Protein Data Bank and is read and written by many programs.
RCSB PDB: Homepage
RCSB Protein Data Bank (RCSB PDB) enables breakthroughs in science and education by providing access and tools for exploration, visualization, and analysis of: These data can be explored in context of external annotations providing a structural view of biology. 3D visualization for PDB structures and ligand binding sites.
wwPDB: File Format - Protein Data Bank
The original PDB format was introduced in 1972 and used a line length of 132 characters plus 8 for sequencing. In 1976, a version using 72 characters plus 8 for sequencing was introduced. This 80-column format is what has commonly been called the (legacy) "PDB format".
PDB-101: Learn: Guide to Understanding PDB Data: Introduction
If you’re new to the world of structural biology, start with Introduction to the PDB. If you have questions about PDB data, several pages will help: The logic for how structures are annotated, classified, and stored is presented in Beginner’s Guide to PDBx/mmCIF Format; The details of atomic coordinates are described in Dealing with Coordinates
The complete PDB file specification provides for a wealth of information, including authors, litera- ture references, and the identification of substructures such as disulfide bonds, helices, sheets, and active
PDB File Format and Content - Protein Structure & S
The "PDB format" file (not the gz-file, a compressed file) is a text file and can be opened by any text editor (including MS Word). Usually, the file is called a "coordinate file" because it contains a list of coordinates for all atoms of the protein structure in …
PDB-101: Learn: Guide to Understanding PDB Data: PDB Overview
These files are available in several formats (PDB, mmCIF, XML). A typical PDB formatted file includes a large "header" section of text that summarizes the protein, citation information, and the details of the structure solution, followed by the sequence and a …
Beginner’s Guide to PDB Structures and the PDBx/mmCIF Format
The PDBx/mmCIF file format and data dictionary is the basis of wwPDB data deposition, annotation, and archiving of PDB data from all supported experimental methods. This PDB-101 resource is intended as an introductory guide.
FORMAT (6A1,1X,A3,2X,A1,I4,A1,2X,I5,5X,40A1) Note: HET records are used to describe non-standard residues, prosthetic groups, inhib-itors, solvent molecules (except water), etc. The Protein Data Bank attempts to use uniform atom nomenclature for HET groups, as illustrated for some commonly occurring groups in Appendix B.
wwPDB Format version 3.3: Introduction - Protein Data Bank
The Protein Data Bank (PDB) is an archive of experimentally determined three-dimensional structures of biological macromolecules that serves a global community of researchers, educators, and students.
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