Conserved Domains and Protein Classification
[15 FEB 2014] A new version of the Conserved Domain Database (CDD) has been released. Version 3.11 contains 596 new or updated NCBI-curated domain models and now contains the most recent Pfam release 27. Also, position-specific scoring matrices (PSSMs) have been re-computed for many models in CDD, and frequency tables have been added to the PSSMs. The search databases distributed as part of this release can now be used with the composition-based scoring that is now available in the more recent versions of RPS-BLAST (version 2.2.28 and up). The new search databases also remain compatible with previous versions of RPS-BLAST. You can access CDD from http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml and find updated content on the CDD FTP site at ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd. Database statistics, showing the number of domain models from each source database, are provided on the CDD News page.
[12 FEB 2014] The display style for drawing domain models in CD-Search, Batch CD-Search, and CDART has been revised. The display style is now uniform among those tools, with a given domain model rendered in the same shape and color by all three tools. Additionally, a new display option, "Standard Results," is available in CD-Search and Batch CD-Search, and shows the top-scoring domain model from each source database. The Batch CD-Search graphical display of search results also offers a new "compact mode," which displays the domain architecture of each query sequence on a single line. This display type is particularly useful if you select two or more query sequences from the list and want to compare their domain architectures. All three tools (CD-Search, Batch CD-Search, and CDART) employ the latest version of RPS-BLAST, which, as of version 2.2.28, uses composition-based scoring and abolishes the need to mask out compositionally biased regions in query sequences. Live and pre-computed searches generated by the CD-Search web tool now use these settings, and as a result the domain annotations have changed for a number of protein sequences in Entrez.