MMDB: Entrez's 3D-structure database

• Published in: Nucleic acids research 2003-01, Vol.31 (1), p.474-477
• Main Authors: Chen, Jie, Anderson, John B., DeWeese-Scott, Carol, Fedorova, Natalie D., Geer, Lewis Y., He, Siqian, Hurwitz, David I., Jackson, John D., Jacobs, Aviva R., Lanczycki, Christopher J., Liebert, Cynthia A., Liu, Chunlei, Madej, Thomas, Marchler-Bauer, Aron, Marchler, Gabriele H., Mazumder, Raja, Nikolskaya, Anastasia N., Rao, Bachoti S., Panchenko, Anna R., Shoemaker, Benjamin A., Simonyan, Vahan, Song, James S., Thiessen, Paul A., Vasudevan, Sona, Wang, Yanli, Yamashita, Roxanne A., Yin, Jodie J., Bryant, Stephen H.
• Format: Article
• Language: English
• Subjects: Animals; Computer Graphics; Databases, Protein; Imaging, Three-Dimensional; Models, Molecular; Protein Structure, Tertiary; Proteins - chemistry; Structural Homology, Protein
• ISSN: 0305-1048; 1362-4962; 1362-4962
• DOI: 10.1093/nar/gkg086

Three-dimensional structures are now known within most protein families and it is likely, when searching a sequence database, that one will identify a homolog of known structure. The goal of Entrez's 3D-structure database is to make structure information and the functional annotation it can provide easily accessible to molecular biologists. To this end, Entrez's search engine provides several powerful features: (i) links between databases, for example between a protein's sequence and structure; (ii) pre-computed sequence and structure neighbors; and (iii) structure and sequence/structure alignment visualization. Here, we focus on a new feature of Entrez's Molecular Modeling Database (MMDB): Graphical summaries of the biological annotation available for each 3D structure, based on the results of automated comparative analysis. MMDB is available at: http://www.ncbi.nlm.nih.gov/Entrez/structure.html.