1.5. 3D Structural Information for Genomics

Responsible: Jürgen Sühnel, Jena Centre for Bioinformatics.

Background:

Despite various attempts to make information on three-dimensional (3D) structures available to functional genomics resources, the situation is still far from satisfying. All too often is 3D structural information not included or restricted to nothing more than links to a  structural database. We intend to bridge this gap by mapping many kinds of ‘omics’ and other disease-related data onto 3D structures.

Planned work:

The primary part of this project consists in the mapping of ‘omics’ data to 3D structures, including the development of new analysis tools. Examples of such data are: genetic information such as intron-exon boundaries, alternative splice sites, SNP data, post-translational modifications such as glycosylation sites, phosphorylation sites, recognition sites, PROSITE motifs, etc. Some of these mappings exist already elsewhere (for example, the PROSITE mapping in PDBsum: www.biochem.ucl.ac.uk/bsm/pdbsum/ or the ProSAT - Protein Structure Annotation Tool: projects.villa-bosch.de/dbase/pdba/). However, here several existing mapping schemes will be combined, supplemented by new ones and made available within one resource. When doing this type of analysis, we will also investigate correlations between gene and protein structure that may lead to new insights into origin and evolution of introns. The mapping results will be integrated, visualized and made available via our IMB Jena Image Library database (www.imb-jena.de/IMAGE.html). In addition, the role of disease-related information that is already taken into account to some extent in the database, via information from the OMIM (Online Mendelian Inheritance in Man) database, for example, will be reinforced. These value-added 3D structural data can then, for example, be used for an improved genomic annotation. These resources will be developed with the bench biologist/medical researcher in mind.