EMBL-EBI will train researchers from Masaryk University (MU, part of ELIXIR Czech Republic) in the annotation of data in the Protein Databank in Europe (PDBe). The goal is to build local capacity for annotation of PDBe data in the Czech Republic and lay the groundwork for a long-term partnership in data annotation between EMBL-EBI and Masaryk University (MU).
The project is funded by ELIXIR, as part of its Capacity building activities and will serve as a test case in developing the ELIXIR Staff exchange programme.
This six-month project will start in July 2016. In the initial phase, five graduate students from MU will visit the EMBL-EBI campus in Hinxton, UK, and receive training in annotation of PDBe data. After that, the MU group will contribute to the standardisation of names for macromolecular complexes in PDBe.
"Harmonisation of names for macromolecules will allow us to add another layer of biological context to existing structural information in PDB, and provide better service to our users," explains Sameer Velankar, the PDBe Team leader. “For example, researchers in protein synthesis may want to look up and compare the different structures of ribosome. Standard naming convention will make the task much easier and quicker."
Radka Svobodova, Head of Chemoinformatics and bioinformatics team at MU and coordinator of the Czech annotation team, said: "I am delighted to see the collaboration with PDBe take off. In the short term, it will increase our expertise in data annotation, in the long term it will help us strengthen our current collaboration with PDBe and establish a local group that will regularly contribute to annotation and validation of PDBe data."
The experience from the PDBe-MU collaboration will also feed back to ELIXIR Capacity building programme. It will help ELIXIR Hub define the scope and principles for the ELIXIR Staff exchange programme. The programme will support staff visits among ELIXIR Nodes to strengthen links between ELIXIR Nodes in developing local bioinformatics capacities.
PDBe is a founding member of worldwide Protein data Bank (wwPDB), the organisation that manages the single worldwide archive of macromolecular structures the Protein data Bank (PDB). Over the last decade the focus of PDBe team has been on improving data quality and integration of macomolecular structure data with biological information. Towards these efforts, PDBe and UniProt teams collaborate on maintaining the Structure integration with Function, Taxonomy and Sequences resource (SIFTS; http://pdbe.org/sifts) to provide value added information for macromolecular structure data. The team has developed many advanced tools and services to present biomacromolecular structures in the context of biological information.
Masaryk University in Brno, Czech Republic, is one of the leading higher education institutions and the second-largest public university in the country.
The University's National Centre of Biomolecular Research (NCBR) is one of the top Czech laboratories in structural biology and biomolecular research, with access to the best-equipped crystallography laboratories in the country. It is the fist institute in the Czech Republic to offer study programmes in Biomolecular chemistry (masters and doctoral programme) and Chemoinformatics and bioinformatics (undergraduate and masters programme).
The key group in NCBR is the Laboratory of computational chemistry - part of the Chemoinformatics and bioinformatics team - which focuses on the development of software tools and methodologies for validation, annotation, extraction, comparison and characterization of biomacromolecular fragments. The tools already developed include MotiveValidator, ValidatorDB and MOLE.