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Open Access Software

PDBalert: automatic, recurrent remote homology tracking and protein structure prediction

Vatsal Agarwal1, Michael Remmert2, Andreas Biegert2 and Johannes Söding2*

Author Affiliations

1 Department of Biotechnology, Indian Institute of Technology, Roorkee 247667, India

2 Gene Center Munich and Center for Integrated Protein Science (CIPSM), Dept. of Chemistry and Biochemistry, Ludwig-Maximilians-Universtät München, Feodor-Lynen-Str. 25, 81377 Munich, Germany

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BMC Structural Biology 2008, 8:51  doi:10.1186/1472-6807-8-51

Published: 25 November 2008

Abstract

Background

During the last years, methods for remote homology detection have grown more and more sensitive and reliable. Automatic structure prediction servers relying on these methods can generate useful 3D models even below 20% sequence identity between the protein of interest and the known structure (template). When no homologs can be found in the protein structure database (PDB), the user would need to rerun the same search at regular intervals in order to make timely use of a template once it becomes available.

Results

PDBalert is a web-based automatic system that sends an email alert as soon as a structure with homology to a protein in the user's watch list is released to the PDB database or appears among the sequences on hold. The mail contains links to the search results and to an automatically generated 3D homology model. The sequence search is performed with the same software as used by the very sensitive and reliable remote homology detection server HHpred, which is based on pairwise comparison of Hidden Markov models.

Conclusion

PDBalert will accelerate the information flow from the PDB database to all those who can profit from the newly released protein structures for predicting the 3D structure or function of their proteins of interest.