Ligand validation for the Protein Data Bank
نویسندگان
چکیده
منابع مشابه
Validation of Structures in the Protein Data Bank
The Worldwide PDB recently launched a deposition, biocuration, and validation tool: OneDep. At various stages of OneDep data processing, validation reports for three-dimensional structures of biological macromolecules are produced. These reports are based on recommendations of expert task forces representing crystallography, nuclear magnetic resonance, and cryoelectron microscopy communities. T...
متن کاملThe Protein Data Bank
The Protein Data Bank [PDB; Berman, Westbrook et al. (2000), Nucleic Acids Res. 28, 235-242; http://www.pdb.org/] is the single worldwide archive of primary structural data of biological macromolecules. Many secondary sources of information are derived from PDB data. It is the starting point for studies in structural bioinformatics. This article describes the goals of the PDB, the systems in pl...
متن کاملDevelopment of application tools for protein-ligand interaction analyses in Protein Data Bank
The Protein Data Bank (PDB) is the representative database of biomolecular structures, and it contains the richest information of molecular interactions in atomic detail. The number of current entries in PDB has become 52,535, and they contain a total of 8,499 different types of non-protein molecule (ligand) as of Aug, 2008. Various methods have been proposed to take advantage of the accumulate...
متن کاملImplementing an X-ray validation pipeline for the Protein Data Bank
There is an increasing realisation that the quality of the biomacromolecular structures deposited in the Protein Data Bank (PDB) archive needs to be assessed critically using established and powerful validation methods. The Worldwide Protein Data Bank (wwPDB) organization has convened several Validation Task Forces (VTFs) to advise on the methods and standards that should be used to validate al...
متن کاملA New Generation of Crystallographic Validation Tools for the Protein Data Bank
This report presents the conclusions of the X-ray Validation Task Force of the worldwide Protein Data Bank (PDB). The PDB has expanded massively since current criteria for validation of deposited structures were adopted, allowing a much more sophisticated understanding of all the components of macromolecular crystals. The size of the PDB creates new opportunities to validate structures by compa...
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ژورنال
عنوان ژورنال: Acta Crystallographica Section A Foundations and Advances
سال: 2018
ISSN: 2053-2733
DOI: 10.1107/s0108767318096770