%0 Journal Article
%T PDBalert: automatic, recurrent remote homology tracking and protein structure prediction
%A Vatsal Agarwal
%A Michael Remmert
%A Andreas Biegert
%A Johannes S£¿ding
%J BMC Structural Biology
%D 2008
%I BioMed Central
%R 10.1186/1472-6807-8-51
%X 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.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.With the advent of remote homology detection methods relying on the pairwise comparison of sequence profiles, automatic protein structure prediction has become reliable and sensitive enough to be of more general use[1]. For more than half of all proteins in representative genomes, at least one domain can be modelled with decent accuracy by fully automatic methods [[2]; J. Soeding, unpublished data]. When no template can be identified, the user will typically rely on keyword tracking services or regular manual checks of the PDB[3] to find out if a related structure has been released. But keyword searches will miss most of the useful templates, since paralogous proteins generally have different names while most will be sufficiently related to serve as templates for homology modelling or to generate hypotheses about possible functions.Several freely available automatic systems have been developed to perform sequence searches periodically and to notify users about interesting hits. Earlier tools use BLAST[4] to search Swiss-Prot[5] or the non-redundant sequence database at the NCBI: Swiss-Shop[6], DBWatcher[7], BLAST Search Updater[8], and Sequence Alerting System[9]. FastAlert[10] uses FASTA[11] to search the Swiss-Prot, EMBL data library and GenBank data
%U http://www.biomedcentral.com/1472-6807/8/51