Sponsor: Rubicon Genomics
Recording Date: 2/19/2014
Recording Time: 1 hour
We are looking for an outstanding, highly motivated Postdoctoral fellow to join the Thornton group at the European Bioinformatics Institute (EMBL-EBI) located on the Wellcome Trust Genome Campus near Cambridge in the UK.
One of the Thornton Group's collaborations is a consortium called the Midwest Center for Structural Genomics (MCSG, http://www.mcsg.anl.gov). This comprises 7 groups located in the US, UK and Canada and focuses on high-throughput structure determination of proteins of biological interest - particularly those relevant to tackling human disease.
As part of the consortium, the Group has developed a number of computational tools to assist crystallographers and biologists, both within the consortium and elsewhere. The most recent tool is a web server called LigSearch (http://www.ebi.ac.uk/thornton-srv/databases/LigSearch) which aims to identify small molecules that are likely to bind to a given protein. The server takes the protein sequence and searches various databases, including ChEMBL and the PDB, to provide a ranked list of likely binders. Its purpose is to help crystallographers preparing to solve the 3D structure of a new protein identify which small molecules are worth trying. A protein-ligand complex often provides valuable biological information on the protein's natural binding site and the ligand interactions it makes.
There will be scope for the successful candidate for improving and expanding the server. At present, the system uses only the protein sequence, but in cases where the structure is known this might provide a richer and more reliable source of information on binding compounds. Secondly, a more chemistry-aware filter of the output is required to eliminate volatile compounds. Third, the hits need to be screened against a database of commercially available molecules, such as ZINC, to indicate which are readily purchasable and their cost. The system might also have applications in related areas, and further research is needed in collaboration with experimental groups to assess the quality of the system's results. Some improvements to the current system to make it more robust will also need to be made. A small part of the work will involve using the ProFunc program (http://www.ebi.ac.uk/thornton-srv/database/profunc to functionally annotate new MCSG structures.
We are looking for a person with both biological knowledge and programming skills. The former needs to be in the area of protein structure analysis, together with a thorough knowledge of the chemistry of small molecules. The latter should involve, at the very least, a significant working knowledge and experience of a programming language, such as C or Java, and a scripting knowledge such as Perl or Python.
The post-holder should enjoy working in a highly collaborative and interdisciplinary environment. Good written and oral communications skills are essential.
Please apply online through www.embl.org/jobs
The EBI is part of the European Molecular Biology Laboratory (EMBL) and is a world-leading bioinformatics centre providing biological data to the scientific community with expertise is data storage, analysing and representation. EMBL-EBI provides a dynamic, international working environment and has close ties with both the University of Cambridge and the Wellcome Trust Sanger Institute. EMBL-EBI staff enjoy many benefits including excellent sports facilities, a free shuttle bus to Cambridge and other nearby centres, an active sports and social club and an attractive working environment set in 55 acres of parkland