The distribution and query systems of the RCSB Protein Data Bank

@article{Bourne2004TheDA,
  title={The distribution and query systems of the RCSB Protein Data Bank},
  author={Philip E. Bourne and Kenneth J. Addess and Wolfgang Bluhm and Li Chen and Nita Deshpande and Zukang Feng and Ward Fleri and Rachel Kramer Green and Jeffrey C. Merino-Ott and Wayne Townsend-Merino and Helge Weissig and John D. Westbrook and Helen M. Berman},
  journal={Nucleic acids research},
  year={2004},
  volume={32 Database issue},
  pages={
          D223-5
        }
}
The Protein Data Bank (PDB; http://www.pdb.org) is the primary source of information on the 3D structure of biological macromolecules. The PDB's mandate is to disseminate this information in the most usable form and as widely as possible. The current query and distribution system is described and an alpha version of the future re-engineered system introduced. 
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The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema
TLDR
The Research Collaboratory for Structural Bioinformatics (RCSB) has completely redesigned its resource for the distribution and query of 3D structure data, expanding the functionality of the existing site by providing structure data in greater detail and uniformity, improved query and enhanced analysis tools.
Using the Tools and Resources of the RCSB Protein Data Bank
TLDR
The options and procedures for searching and downloading structural data from the PDB, which is maintained by the Research Collaboratory for Structural Bioinformatics (RCSB), are described here along with tools for depositing and assessing the quality of structures.
Using the Tools and Resources of the RCSB Protein Data Bank
TLDR
The options and procedures for searching and downloading structural data from the Research Collaboratory for Structural Bioinformatics (RCSB) PDB are described here, along with tools for assessing the quality of structures.
DIAL: a web-based server for the automatic identification of structural domains in proteins
TLDR
DIAL is a web server for the automatic identification of structural domains given the 3D coordinates of a protein that can examine crystallographic multiple chains and provide structural domain solutions that can also describe domain swapping events.
The SSEA server for protein secondary structure alignment
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A web server that computes alignments of protein secondary structures that supports both performing pairwise alignments and searching a secondary structure against a library of domain folds and can calculate global and local secondary structure element alignments.
Citing a Data Repository: A Case Study of the Protein Data Bank
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A novel metric based on information cascade constructed by exploring the citation network to measure influence between competing works is described and applied to analyze different data citation practices to PDB.
RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D
TLDR
How the archive is growing and evolving as new experimental methods generate ever larger and more complex biomolecular structures is described; the importance of data standards and data remediation in effective management of the archive and facile integration with more than 50 external data resources are described.
STRIDE: a web server for secondary structure assignment from known atomic coordinates of proteins
TLDR
STRIDE is a software tool for secondary structure assignment from atomic resolution protein structures that makes combined use of hydrogen bond energy and statistically derived backbone torsional angle information and is optimized to return resulting assignments in maximal agreement with crystallographers' designations.
iPfam: visualization of protein?Cprotein interactions in PDB at domain and amino acid resolutions
TLDR
A web resource is implemented that allows the investigation of protein interactions in the Protein Data Bank structures at the level of Pfam domains and amino acid residues.
The HHpred interactive server for protein homology detection and structure prediction
HHpred is a fast server for remote protein homology detection and structure prediction and is the first to implement pairwise comparison of profile hidden Markov models (HMMs). It allows to search a…
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