| Literature DB >> 12520028 |
Aron Marchler-Bauer1, John B Anderson, Carol DeWeese-Scott, Natalie D Fedorova, Lewis Y Geer, Siqian He, David I Hurwitz, John D Jackson, Aviva R Jacobs, Christopher J Lanczycki, Cynthia A Liebert, Chunlei Liu, Thomas Madej, Gabriele H Marchler, Raja Mazumder, Anastasia N Nikolskaya, Anna R Panchenko, Bachoti S Rao, Benjamin A Shoemaker, Vahan Simonyan, James S Song, Paul A Thiessen, Sona Vasudevan, Yanli Wang, Roxanne A Yamashita, Jodie J Yin, Stephen H Bryant.
Abstract
The Conserved Domain Database (CDD) is now indexed as a separate database within the Entrez system and linked to other Entrez databases such as MEDLINE(R). This allows users to search for domain types by name, for example, or to view the domain architecture of any protein in Entrez's sequence database. CDD can be accessed on the WorldWideWeb at http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=cdd. Users may also employ the CD-Search service to identify conserved domains in new sequences, at http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi. CD-Search results, and pre-computed links from Entrez's protein database, are calculated using the RPS-BLAST algorithm and Position Specific Score Matrices (PSSMs) derived from CDD alignments. CD-Searches are also run by default for protein-protein queries submitted to BLAST(R) at http://www.ncbi.nlm.nih.gov/BLAST. CDD mirrors the publicly available domain alignment collections SMART and PFAM, and now also contains alignment models curated at NCBI. Structure information is used to identify the core substructure likely to be present in all family members, and to produce sequence alignments consistent with structure conservation. This alignment model allows NCBI curators to annotate 'columns' corresponding to functional sites conserved among family members.Entities:
Mesh：
Year: 2003 PMID： 12520028 PMCID： PMC165534 DOI： 10.1093/nar/gkg087
Source DB: PubMed Journal: Nucleic Acids Res ISSN： 0305-1048 Impact factor: 16.971