European Molecular Biology Laboratory


November 8, 2021


Bioinformatician Location: EMBL-EBI, Hinxton near Cambridge, UK

Staff Category: Staff Member Contract Duration: approximately 3 years (estimated 01/02/2022-30/01/2025) Grading: Grade 5 or 6 (monthly salary starting at £2,809 or £3,143 per month after tax) plus benefits Closing Date: 8 November 2021 Reference Number: EBI01923

We are looking for a structural bioinformatician who is interested in developing methods for protein structure analysis to identify biologically relevant conformational states and link these to macromolecular function. The post holder will join the Velankar team at EMBL-EBI on a 3-year collaborative project between Protein Data Bank in Europe (PDBe) and CCP4. They will implement new data analysis methods, improve biological data processing pipelines, perform data analysis, and contribute to developing user-facing web pages. This is the role for you if you are someone who is creative, curious, and ambitious with a drive to tackle impactful biological data analysis problems.

The Velankar team maintains macromolecular structure databases that form essential resources for biologists and other life-scientists worldwide, including the Protein Data Bank as a founding partner of the Worldwide Protein Data Bank organisation (wwPDB;, PDBe Knowledge Base that integrates structural and functional annotations and the AlphaFold Protein Structure Database in collaboration with DeepMind. The PDBe team consists of an international and inter-disciplinary team (data curators, bioinformaticians, scientific software developers and IT specialists).

Your role

You will be in a scientific, technical role. You will work together with developers from PDBe and CCP4 to enhance the structure superposition tool GESAMT.

In this role, you will:

  • help define data standards and influence the algorithm development for the superposition of ligand binding sites, protein chains, and macromolecular assemblies;
  • build upon and maintain one of our internal data pipelines, generating superposed structures and clusters for the complete PDB archive;
  • have an experimental, innovation-driven mindset and investigate the biological relevance of distinct conformational groups, designing methods for annotating these clusters;
  • be interested in designing and developing user-facing web pages to display superposed structures to provide researchers with a larger biological context of protein structures in the PDB.
  • You have
  • MSc or PhD in bioinformatics or related fields
  • A proven track record of data analysis using Python libraries
  • Experience in protein superposition
  • Experience in creating production-grade data pipelines
  • Proficiency in Python3+
  • Knowledge of PDB data formats
  • Excellent written and oral English skills
  • You might also have
  • Scientific publications on the field of protein/nucleic acid superpositions
  • Experience with programmatic access frameworks (e.g. FastAPI)
  • Knowledge of front-end development with experience in HTML5, CSS3, JS/TS
  • Experience in presenting scientific themes at conferences and/or workshops
  • Why join us

    Do something meaningful AtEMBL-EBI you can apply your talent and passion to accelerate science and tackle some of humankind's greatest challenges. EMBL-EBI, part of the European Molecular Biology Laboratory, is a worldwide leader in the storage, analysis and dissemination of large biological datasets. We provide the global research community with access to publicly available databases and tools which are crucial for the advancement of healthcare, food security, and biodiversity. Join a culture of innovation We are located on the Wellcome Genome Campus, alongside other prominent research and biotech organisations, and surrounded by beautiful Cambridgeshire countryside. This is a highly collaborative and inclusive community where our employees enjoy a relaxed atmosphere. We are committed to ensuring our employees feel valued, supported and empowered to reach their professional potential. Enjoy lots of benefits:

  • Financial incentives: Monthly family, child and non-resident allowances, annual salary review, pension scheme including 17% employer contribution, death benefit, long-term care, accident-at-work and unemployment insurances
  • Flexible working arrangements
  • Private medical insurance for you and your immediate family (including all prescriptions and generous dental & optical cover)
  • Generous time off: 30 days annual leave per year, in addition to eight bank holidays
  • Relocation package including installation grant (if required
  • Campus life: Free shuttle bus to and from work, on-site library, subsidised on-site gym and cafeteria, casual dress code, extensive sports and social club activities (on campus and remotely)
  • Family benefits : On-site nursery, 10 days of child sick leave, generous parental leave, holiday clubs on campus and monthly family and child allowances
  • Benefits for non-UK residents: Visa exemption, education grant for private schooling, financial support to travel back to your home country every second year and a monthly non-resident allowance.
  • For more details please see our employee benefits page.

    What else you need to know
  • Contract duration: This position is a grant/project-limited fixed-term contract foreseen for a duration of 3 years until anticipated completion date of 30/01/2025 (whichever is shortest).
  • International applicants: We recruit internationally and successful candidates are offered visa exemptions. Read more on our page for international applicants.
  • Diversity and inclusion : At EMBL-EBI, we strongly believe that inclusive and diverse teams benefit from higher levels of innovation and creative thought. We encourage applications from women, LGBTQ+ and individuals from all nationalities.
  • Job location: This role is based in Hinxton, UK and you will be required to relocate once it is safe to do so, if you are currently based abroad. Read more about how we are recruiting during the pandemic.
  • Your application : To apply please submit a cover letter and a CV through our online system. We aim to provide a response within two weeks after the closing date: 08 November 2021.