Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2007 Jan;35(Database issue):D298-300.
doi: 10.1093/nar/gkl952. Epub 2006 Nov 29.

MMDB: annotating protein sequences with Entrez's 3D-structure database

Yanli Wang  1 , Kenneth J Addess, Jie Chen, Lewis Y Geer, Jane He, Siqian He, Shennan Lu, Thomas Madej, Aron Marchler-Bauer, Paul A Thiessen, Naigong Zhang, Stephen H Bryant
Affiliations

MMDB: annotating protein sequences with Entrez's 3D-structure database

Yanli Wang et al. Nucleic Acids Res. 2007 Jan.

Abstract

Three-dimensional (3D) structure is now known for a large fraction of all protein families. Thus, it has become rather likely that one will find a homolog with known 3D structure when searching a sequence database with an arbitrary query sequence. Depending on the extent of similarity, such neighbor relationships may allow one to infer biological function and to identify functional sites such as binding motifs or catalytic centers. Entrez's 3D-structure database, the Molecular Modeling Database (MMDB), provides easy access to the richness of 3D structure data and its large potential for functional annotation. Entrez's search engine offers several tools to assist biologist users: (i) links between databases, such as between protein sequences and structures, (ii) pre-computed sequence and structure neighbors, (iii) visualization of structure and sequence/structure alignment. Here, we describe an annotation service that combines some of these tools automatically, Entrez's 'Related Structure' links. For all proteins in Entrez, similar sequences with known 3D structure are detected by BLAST and alignments are recorded. The 'Related Structure' service summarizes this information and presents 3D views mapping sequence residues onto all 3D structures available in MMDB (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=structure).

PubMed Disclaimer

Figures

Figure 1
Figure 1
Non-identical protein sequences in Entrez have been classified into groups linked to related structures, at various levels of sequence similarity. Sequence identity is calculated from the BLAST alignments, and here only those neighbor relationships are listed that produce an aligned footprint of 50 residues or more. The analysis also excludes protein sequences which have been directly obtained from MMDB. Forty-eight percent of sequences in Entrez protein have at least one structure neighbor with an extensive alignment footprint and at least 30% identical residues.
Figure 2
Figure 2
A screen shot of the ‘Related Structure’ summary along with Entrez's document summary for protein NP_036676. Clicking on the ‘Related Structure’ option from the ‘Links’ pull-down menu launches the summary view.
Figure 3
Figure 3
A Cn3D view of the query sequence from Figure 2 aligned to chain A of the related structure 1O86 (PDB code). Residues in aligned regions are displayed in upper case letters with identical residue pairs rendered in red color. Residues within a 5 A contact radius of the bound drug lisinopril are highlighted in the 3D structure view and automatically mapped onto the aligned residues shown in the sequence alignment window. Side chains of these residues are displayed selectively and rendered as ball-and-stick models.
See this image and copyright information in PMC

Similar articles

  • MMDB: Entrez's 3D-structure database.
    Wang Y, Anderson JB, Chen J, Geer LY, He S, Hurwitz DI, Liebert CA, Madej T, Marchler GH, Marchler-Bauer A, Panchenko AR, Shoemaker BA, Song JS, Thiessen PA, Yamashita RA, Bryant SH. Wang Y, et al. Nucleic Acids Res. 2002 Jan 1;30(1):249-52. doi: 10.1093/nar/30.1.249. Nucleic Acids Res. 2002. PMID: 11752307 Free PMC article.
  • MMDB: Entrez's 3D-structure database.
    Chen J, Anderson JB, DeWeese-Scott C, Fedorova ND, Geer LY, He S, Hurwitz DI, Jackson JD, Jacobs AR, Lanczycki CJ, Liebert CA, Liu C, Madej T, Marchler-Bauer A, Marchler GH, Mazumder R, Nikolskaya AN, Rao BS, Panchenko AR, Shoemaker BA, Simonyan V, Song JS, Thiessen PA, Vasudevan S, Wang Y, Yamashita RA, Yin JJ, Bryant SH. Chen J, et al. Nucleic Acids Res. 2003 Jan 1;31(1):474-7. doi: 10.1093/nar/gkg086. Nucleic Acids Res. 2003. PMID: 12520055 Free PMC article.
  • MMDB: 3D structure data in Entrez.
    Wang Y, Addess KJ, Geer L, Madej T, Marchler-Bauer A, Zimmerman D, Bryant SH. Wang Y, et al. Nucleic Acids Res. 2000 Jan 1;28(1):243-5. doi: 10.1093/nar/28.1.243. Nucleic Acids Res. 2000. PMID: 10592236 Free PMC article.
  • From protein sequences to 3D-structures and beyond: the example of the UniProt knowledgebase.
    Hinz U; UniProt Consortium. Hinz U, et al. Cell Mol Life Sci. 2010 Apr;67(7):1049-64. doi: 10.1007/s00018-009-0229-6. Epub 2009 Dec 31. Cell Mol Life Sci. 2010. PMID: 20043185 Free PMC article. Review.
  • Protein structure databases.
    Laskowski RA. Laskowski RA. Mol Biotechnol. 2011 Jun;48(2):183-98. doi: 10.1007/s12033-010-9372-4. Mol Biotechnol. 2011. PMID: 21225378 Review.
See all similar articles

Cited by

See all "Cited by" articles

References

    1. Wheeler D.L., Barrett T., Benson D.A., Wheeler D.L., Barrett T., Benson D.A., Bryant S.H., Canese K., Chetvernin V., Church D.M., et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2006;34:D173–D180. - PMC - PubMed
    1. Deshpande N., Addess K.J., Bluhm W.F., Merino-Ott J.C., Townsend-Merino W., Zhang Q., Knezevich C., Xie L., Chen L., Feng Z., et al. The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema. Nucleic Acids Res. 2005;33:D233–D237. - PMC - PubMed
    1. Ohkawa H., Ostell J., Bryant S. MMDB: an ASN.1 specification for macromolecular structure. Proc. Int. Conf. Intell. Syst. Mol. Biol. 1995;3:259–667. - PubMed
    1. Chen J., Anderson J.B., DeWeese-Scott C., Fedorova N.D., Geer L.Y., He S., Hurwitz D.I., Jackson J.D., Jacobs A.R., Lanczycki C.J., et al. MMDB: Entrez's 3D-structure database. Nucleic Acids Res. 2003;31:474–477. - PMC - PubMed
    1. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25:3389–3402. - PMC - PubMed

Publication types