Bioinformatics just made our latest paper available as an early preview:
Precalculated Protein Structure Alignments at the RCSB-PDB website
Summary: With the continuous growth of the RCSB Protein Data Bank (PDB), Berman et al. (2000), providing an up-to-date systematic structure comparison of all protein structures poses an ever growing challenge. Here we present a comparison tool for calculating both 1D protein sequence and 3D protein structure alignments. This tool supports various applications at the RCSB PDB website. First, a structure alignment web service calculates pairwise alignments. Second, a stand-alone application runs alignments locally and visualizes the results. Third, pre-calculated 3D structure comparisons for the whole PDB are provided and updated on a weekly basis. These three applications allow users to discover novel relationships between proteins available either at the RCSB PDB or provided by the user.
Availability and Implementation: A web user interface is available at
http://www.rcsb.org/pdb/workbench/workbench.do. The source code
is available under the LGPL license from http://www.biojava.org.
A source bundle, prepared for local execution, is available from
UPDATE: the link below should provide free access:
Read the full paper here