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RCSB PDB Newsletter #20: PDB Focus: Redundancy Reduction Cluster Data Available on the PDB FTP Site
HEADLINES

No. 20
Winter 2004


FRONT PAGE

Message from the RCSB PDB

Announcing the Worldwide Protein Data Bank

Downloadable PDB_EXTRACT Makes Deposition Easier

Biological Unit Tutorial Now Available from the RCSB PDB

Ligand Depot--a Small Molecule Information Resource

PDB Focus: Deposition and Release Policies

PDB Deposition Statistics

Lucene Keyword Search Released on the RCSB PDB Web Site

PDB Focus: Redundancy Reduction Cluster Data Available on the PDB FTP Site

PDB Focus: Searching for Experimental Data Files

Updates of mmCIF Files on the RCSB PDB FTP Site

RCSB PDB Web Site Statistics

NIGMS News: PSI-2 and Structural Biology Roadmap RFA

RCSB PDB Article Published in Nucleic Acids Research

New Update Release of CD-ROM Sets

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

Related Links: FTP Resources

RCSB PDB Job Listings

RCSB PDB Members & Statement of Support


Questions? info@rcsb.org

© 2004 RCSB PDB

 

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 home page on the RCSB PDB Web sites.

Files that list the clusters and their rankings at 50%, 70% and 90% sequence identity are available. Smaller rank numbers indicate higher (better) ranking. Chains with rank number 1 are ranked as the best representative of their cluster.

The contents of these files and the details of the clustering and ranking are further described at ftp://ftp.rcsb.org/pub/pdb/derived_data/NR/README and www.rcsb.org/pdb/redundancy.html.