RCSB PDB Newsletter #20

RCSB PDB Newsletter
Number 20 Winter 2004 Published quarterly by the
Research Collaboratory for Structural Bioinformatics
Protein Data Bank

Text-only version PDF version PDB Newsletter archive

January 1, 2004

23,792 released atomic coordinate entries

Molecule Type

21,516 proteins, peptides, and viruses
1,276 nucleic acids
982 protein/nucleic acid complexes
18 carbohydrates

Experimental Technique

20,224 diffraction and other
11,469 structure factor files
3,568 NMR
1,790 NMR restraint files


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Message from the RCSB PDB

Announcing the Worldwide Protein Data Bank Reprinted with permission from Nature Structural Biology.

Data Deposition and Processing

Downloadable PDB_EXTRACT Makes Deposition Easier The software program PDB_EXTRACT was developed to assist depositors in the automatic preparation of crystallographic depositions. This software tool extracts information for deposition from the output files produced by many applications used for structure determination... [MORE...]

Biological Unit Tutorial Now Available from the RCSB PDB An introduction to biological units in the PDB archive is now accessible at www.rcsb.org/pdb/biounit_tutorial.html. This useful guide offers definitions of the terms 'asymmetric unit' and 'biological molecule', indicates where information about the biological unit can be found in PDB and mmCIF coordinate files, and describes how the biological unit files in the PDB have been derived... [MORE...]

Ligand Depot--a Small Molecule Information Resource Ligand Depot (ligand-depot.rutgers.edu) is a data warehouse that integrates databases, services, and tools related to small molecules bound to macromolecules... [MORE...]

PDB Focus: Deposition and Release Policies Guidelines for the deposition of coordinate and experimental data have been set by the IUCr, IUPAC-IUBMB-IUPAB, the NIH, and the journals. These policies are detailed at deposit.pdb.org/#release... [MORE...]

PDB Deposition Statistics

Data Query, Reporting, and Access

Lucene Keyword Search Released on the RCSB PDB Web Site After a period of beta testing, the Lucene keyword search engine has replaced the previously-used LDAP keyword search engine to support text searches on the RCSB PDB home page, SearchLite, and the "Text Search" field on SearchFields. Lucene uses an index of the remediated mmCIF files to return much more accurate keyword search results... [MORE...]

PDB Focus: Redundancy Reduction Cluster Data Available on the PDB FTP Site The results of the weekly clustering of protein chains in the PDB are posted at ftp://ftp.rcsb.org/pub/pdb/derived_data/NR/. These clusters are used in the "remove similar sequences" feature on SearchLite, SearchFields, and the PDB home page on the PDB Web sites... [MORE...]

PDB Focus: Searching for Experimental Data Files The PDB offers several ways to locate experimental data files for structure entries. The SearchFields interface offers an option to narrow a search to only include entries that have experimental data (X-ray structure factors or NMR restraints) available... [MORE...]

Updates of mmCIF Files on the RCSB PDB FTP Site As previously announced, the update of September 2, 2003 included the replacement of all mmCIF files in the RCSB PDB FTP archives with the remediated mmCIF files. Due to our ongoing data curation efforts, occasional weekly updates will include the replacement of large numbers of mmCIF files... [MORE...]

RCSB PDB Web Site Statistics


NIGMS News: PSI-2 and Structural Biology Roadmap RFA Concept Clearance of the PSI-2 Production Phase; Announcement of Structural Biology Roadmap RFA ... [MORE...]

RCSB PDB Article Published in Nucleic Acids Research The article, "The distribution and query systems of the RCSB Protein Data Bank," has been published in the latest issue of Nucleic Acids Research. This feature describes the dissemination and accessibility of PDB data via the current PDB query and distribution system... [MORE...]

New Update Release of CD-ROM Sets The October 2003 update of the PDB CD-ROM data set, Release #106, is an incremental set of 1,583 experimentally determined structures and 61 models. The structure coordinate files, contained on one disk, are shipping now... [MORE...]

PDB Molecules of the Quarter: Trypsin, Simian Virus 40, and Catabolite Activator Protein

PDB Community Focus: Edward N. Baker

PDB Education Corner by Katherine Kantardjieff

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