Integrating electron microscopy information into existing Distributed Annotation Systems.
The increase of daily released bioinformatic data has generated new ways of organising and disseminating information. Specifically, in the field of sequence data, many efforts have been made not only to store information in databases, but also to annotate it and then share these annotations through a standard XML (eXtensible Markup Language) protocol and appropriate integration clients. This is the context in which the Distributed Annotation System (DAS) has emerged in genomics. Additionally, initiatives in the field of structural data, such as the extension of DAS to atomic resolution data, which generated the SPICE client, have also occurred. This paper presents 3D-EM DAS, a further extension of the DAS protocol that allows sharing annotations about hybrid models. This annotation system has been built on the basis of the EMDB, which stores Three-dimensional Electron Microscopy (3D-EM) volumes, PDB, which houses atomic coordinates, and UniProt (for protein sequences) databases. In this way, annotations for sequences, atomic coordinates, and 3D-EM volumes are collected and displayed through a single graphical visualization client. Thus, users have an integrated view of all the annotations together with the whole macromolecule (3D-EM map coming from EMDB), the atomic resolution structures fitted into it (coordinates coming from PDB) and the sequences corresponding to each of the structures (from UniProt).
Macías
J R
JR
Unidad de Biocomputación, Centro Nacional de Biotecnología-CSIC, Campus de Cantoblanco UAM, c/ Darwin 3, 28049 Madrid, Spain. jrmacias@cnb.uam.es
Jiménez-Lozano
N
N
Carazo
J M
JM
D019295:Computational Biology / Q000379:methods*; D003195:Computer Communication Networks; D030562:Databases, Protein; D008854:Microscopy, Electron; D011487:Protein Conformation