SCCJ Cafe –Season 4–Shape of Protein Molecules (4) ”Description of Molecular Structural Information in PDB”

DOI Web Site 1 Citations
  • Kudou Takahiro
    大阪大学蛋白質研究所 日本蛋白質構造データバンク 〒565-0871 大阪府吹田市山田丘3-2

Bibliographic Information

Other Title
  • SCCJ Cafe –Season 4– 分子のかたち (4)「PDBのデータ書式」

Abstract

There are several formats to describe PDB structural data and I introduce them in this article. Each format file is available from the PDBj web site (Figure 1). The most historical format is PDB format (Figure 2). It is 80 columns fixed format and the included information is partial. Moreover it includes some free description sections and it is not suitable for computational processing. As it will be phased out in 2016, it is recommended to use the current canonical format PDBx/mmCIF (Figure 3). It is defined by the extension of STAR format, which can include flexible length of lines. wwPDB also provides XML translated format PDBML (Figure 4). One can use general XML purser for it, but the file size is larger than PDBx/mmCIF. In the PDBx/mmCIF and PDBML, two types of ids for items such as atoms and residues are defined. One is author-defined id, which is not always sequential and may include non-numerical strings. The other is defined by wwPDB, which follows the systematic rule.

Journal

Citations (1)*help

See more

Keywords

Details 詳細情報について

Report a problem

Back to top