MMDB: Entrez's 3D-structure database - PubMed (original) (raw)

. 2003 Jan 1;31(1):474-7.

doi: 10.1093/nar/gkg086.

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, Aron Marchler-Bauer, Gabriele H Marchler, Raja Mazumder, Anastasia N Nikolskaya, Bachoti S Rao, Anna R Panchenko, Benjamin A Shoemaker, Vahan Simonyan, James S Song, Paul A Thiessen, Sona Vasudevan, Yanli Wang, Roxanne A Yamashita, Jodie J Yin, Stephen H Bryant

Affiliations

MMDB: Entrez's 3D-structure database

Jie Chen et al. Nucleic Acids Res. 2003.

Abstract

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.

PubMed Disclaimer

Figures

Figure 1

Figure 1

MMDB's ‘structure summary’ for Hck kinase/1QCF. The location of the intra-molecular interaction of phosphotyrosine with the SH2 domain is highlighted in green.

Figure 2

Figure 2

MMDB's ‘VAST summary’ of selected structure neighbours of the SH2 domain (3D domain 2) of Hck kinase/1QCF. The locations of loop regions whose conformation is conserved in Grb2/1JYR and c-Cbl/1FBV are highlighted in green, as is the phosphotyrosine residue of a peptide bound to 1FBV. Analogous loop regions in acetate-kinase/1G99 are highlighted in yellow. The loop analogous to that near 1QCF K105 adopts a different conformation and the loop analogous to that near 1QCF G75 occludes the site where SH2 domains bind phosphotyrosine. Cn3D's alignment window displays the residues of 1QCF that may be superposed onto all selected neighbours; the degree of sequence conservation is indicated via a colour-ramp from blue-grey to red, with non-aligned sites shown in grey.

Similar articles

Cited by

References

    1. Wheeler D.L., Church,D.M., Lash,A.E., Leipe,D.D., Madden,T.L., Pontius,J.U., Schuler,G.D., Schriml,L.M., Tatusova,T.A. and Wagner. (2003) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 31, 28–33. - PMC - PubMed
    1. Westbrook J., Feng,Z., Jain,S., Bhat,T.N., Thanki,N., Ravichandran,V., Gilliland,G.L., Bluhm,W., Weissig,H., Greer,D.S., Bourne,P.E. and Berman,H.M. (2003) The Protein Data Bank: unifying the archive. Nucleic Acids Res., 31, 489–491. - PMC - PubMed
    1. Wang Y., Anderson,J.B., Chen,J., Geer,L.Y., He,S., Hurwitz,D.I., Liebert,C.A., Madej,T., Marchler,G.H., Marchler-Bauer,A., Panchenko,A.R., Shoemaker,B.A., Song,J.S., Thiessen,P.A., Yamashita,R.A. and Bryant,S.H. (2002) MMDB: Entrez's 3D-structure database. Nucleic Acids Res., 30, 249–252. - PMC - PubMed
    1. Altschul S.F., Madden,T.L., Schaäffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389–3402. - PMC - PubMed
    1. Marchler-Bauer A., Anderson,J., Fedorova,N., DeWeese-Scott,C., Geer,L.Y., He,S., Hurwitz,D.I., Jackson,J.D., Jacobs,A., Lanczycki,C., Liebert,C., Liu,C., Madej,T., Marchler,G.A., Mazumder,R., Nikolskaya,A., Panchenko,A.R., Shoemaker,B.A., Song,J., Rao,R.B., Thiessen,P.A., Vasudevan,S., Wang,Y., Yamashita,R., Yin,J. and Bryant,S.H. (2003) CDD: A curated Entrez database of conserved domain alignments. Nucleic Acids Res., 31, 383–387. - PMC - PubMed

Publication types

MeSH terms

Substances

LinkOut - more resources