Layer, Chiang, et al. Genome Biology
Excellent sporting facilities, a free shuttle bus to campus and other nearby centres and an attractive working environment set in 55 acres of parkland.
We are seeking to recruit a structural analyst/programmer to join the Protein Data Bank in Europe team (PDBe) at the European Bioinformatics Institute located on the Wellcome Trust Genome Campus near Cambridge in the UK.
The Protein Data Bank in Europe (PDBe; pdbe.org) is part of the Worldwide Protein Data Bank organisation (wwPDB; wwpdb.org), which maintains the global archive of 3D structural data on biomacromolecules. The PDBe team also maintains a number of databases that support deposition and advanced search services for structural biologists and the wider scientific community. The team consists of an international and inter-disciplinary mix of professionals (scientists and IT specialists).
Established in 1994, CATH and SCOP are the world’s most comprehensive resources classifying protein-domain structures into evolutionary superfamilies. They are currently being combined in a collaborative project - Genome3D - that aims to provide predicted 3D structures for sequences assigned to SCOP and CATH superfamilies. Combining SCOP and CATH based predictions allows us to identify more accurately regions that agree between the two methods. We aim to provide these Genome3D-predicted structures via the PDBe resource. To improve the assessment of the reliability of the predictions it is necessary to develop a mapping between SCOP and CATH and to remove any conflicts.
We are now seeking to recruit a structural analyst/programmer to assist with this task. The structural analyst/programmer will also build an automatic pipeline to generate putative domain assignments (from CATH) for new PDB structures, prior to classification in SCOP or CATH. The structural analyst/programmer will be based at PDBe, and will be jointly supervised by Prof. Christine Orengo (UCL, London) and Dr Alexey Muzin (MRC-LMB, Cambridge), together with Prof. Gerard Kleywegt and Dr Sameer Velankar at PDBe.
To the successful applicant this post will offer a challenging opportunity to have a real impact on the global efforts to archive and classify 3D protein structures and to exploit these for structural and functional predictions.
The EBI is part of the European Molecular Biology (EMBL-EBI) and is a world-leading bioinformatics centre. We provide a dynamic, international working environment and our 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.
Applicants should have a PhD in some area of structural biology, structural chemistry or structural bioinformatics, and experience of working with the PDB, CATH or SCOP resources. Proven programming skills (e.g., in C/C++ or Java, and Python or Perl) and experience with developing web-based tools and web services are essential. In-depth knowledge and understanding of protein structure is necessary and a few years of post-doctoral research experience in structural biology or structural bioinformatics would be an advantage.
Excellent written and oral communication skills, fluency in English, ability to work independently in a distributed team, and attention to detail are required.