Open AccessAutomated and accurate deposition of structures solved by X‐ray diffraction to the Protein Data Bank
Author(s) -
Yang Huanwang,
Guranovic Vladimir,
Dutta Shuchismita,
Feng Zukang,
Berman Helen M.,
Westbrook John D.
Publication year - 2004
Publication title -
acta crystallographica section d
Language(s) - English
Resource type - Journals
ISSN - 1399-0047
DOI - 10.1107/s0907444904019419
Subject(s) - protein data bank (rcsb pdb) , protein data bank , software , suite , computer science , software suite , deposition (geology) , phaser , data mining , crystallography , chemistry , protein structure , programming language , biology , physics , optics , paleontology , biochemistry , archaeology , sediment , stereochemistry , history
The RCSB Protein Data Bank (PDB) has a number of options for deposition of structural data and has developed software tools to facilitate the process. In addition to ADIT and the PDB Validation Suite , a new software application, pdb_extract , has been designed to promote automatic data deposition of structures solved by X‐ray diffraction. The pdb_extract software can extract information about data reduction, phasing, molecular replacement, density modification and refinement from the output files produced by many X‐ray crystallographic applications. The options, procedures and tools for accurate and automated PDB data deposition are described here.