Pre-calculated protein structure alignments at the RCSB PDB website

By Andreas Prlic, Spencer E. Bliven, Peter W. Rose, Wolfgang Bluhm, C. Bizon, Adam Godzik, Philip E. Bourne. 2010

211 citations recorded by the source corpus.

Summary: With the continuous growth of the RCSB Protein Data Bank (PDB), 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 http://source.rcsb.org Contact: andreas@sdsc.edu; pbourne@ucsd.edu

Subfields: Materials Chemistry, Molecular Biology

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Materials Chemistry

  1. John D. Westbrook
  2. Philip E. Bourne
  3. Christine Zardecki
  4. David S. Goodsell
  5. Shuchismita Dutta
  6. Andreas Prlic
  7. Helen M. Berman
  8. Peter W. Rose

In Molecular Biology

  1. John D. Westbrook
  2. Philip E. Bourne
  3. David S. Goodsell
  4. Christine Zardecki
  5. Shuchismita Dutta
  6. Andreas Prlic
  7. Helen M. Berman
  8. Peter W. Rose

Citations in the corpus