Bioinformatician in Saffron Walden

We are seeking a Bioinformatician with expertise in data integration and experience in structural biology and molecular dynamics (MD) data to join the Velankar team at the European Bioinformatics Institute (EMBL-EBI). The Protein Data Bank in Europe (PDBe) team develops essential macromolecular structure resources and tools for biologists and other life scientists. As a founding partner of the Worldwide Protein Data Bank, we are responsible for maintaining the global archive of experimentally determined macromolecular structures, the Protein Data Bank (PDB). We also manage the community-led PDBe Knowledge Base (PDBe-KB) resource and the AlphaFold Protein Structure Database (AFDB), a collaboration with Google DeepMind.

This position offers an exciting opportunity to contribute to the Horizon Europe-funded MD4SB (Molecular Dynamics for Structure-Based Biology) project. MD4SB is a major European research infrastructure initiative aiming to transform structural biology by integrating molecular dynamics simulation data into the wider life sciences ecosystem.

Your role will involve:

• Contributing to the development of infrastructure connecting molecular dynamics simulations with structural biology resources and biological knowledge bases.
• Developing AI-driven approaches to mine scientific literature and automatically extract experimental and biological metadata to enrich MD datasets.
• Developing and extending SIFTS (Structure Integration with Function, Taxonomy and Sequence), a core PDBe resource that provides residue-level mappings between PDB structures, UniProtKB sequences, and other biological resources.

This is an interdisciplinary role combining structural bioinformatics, molecular dynamics, and scientific software development. You will apply both scientific understanding and technical expertise to develop data integration workflows, APIs, and biological annotations that improve interoperability and reuse of structural and molecular simulation data across various resources.

Primary responsibilities include:

• Designing and implementing data integration pipelines that connect MDDB with major life science resources, including PDBe, UniProt, PDBe-KB, and other relevant knowledge bases and databases.
• Developing and deploying AI- and machine learning-based approaches for extracting experimental and biological metadata from scientific literature to enrich MDDB datasets.
• Extending and maintaining the SIFTS infrastructure and codebase.
• Developing and maintaining software tools, APIs, workflows, and documentation that facilitate FAIR data integration.
• Collaborating with domain experts, software engineers, and data resource providers.
• Supporting FAIRification, standardisation, and interoperability of MD datasets and associated annotations.
• Participating in community standards development, technical documentation, training, outreach, and dissemination activities.

You have:

• PhD in Bioinformatics, Computational Biology, Structural Biology, Computer Science, Data Science, or a related field.
• Familiarity with structural biology and molecular simulation data.
• Experience with NLP/LLM-based scientific literature mining.
• Demonstrated experience with FAIR data principles, metadata standards, and scientific repositories.
• Understanding of sequence, structure, and functional annotations of proteins.
• Experience in scientific software development, preferably in Python.
• Experience with Linux environments, Git, and CI/CD practices.
• Strong communication, collaboration, and problem-solving skills.

You may also have:

• Postdoctoral research experience in a relevant field.
• Experience with graph databases (e.g. Neo4J), REST APIs, containerisation technologies, and workflow management systems such as Nextflow.
• Experience in data visualisation and analysis.
• Understanding of FAIR data principles and the biological data lifecycle.
• Experience in reporting and presenting scientific topics.
• Experience working in international and interdisciplinary teams.

Benefits and Contract Information:

• Financial incentives: monthly family/marriage allowance, child allowance, non-resident allowance, annual salary review, pension scheme, and insurances.
• Hybrid working arrangements.
• Private medical insurance for you and your immediate family.
• Generous time off: 30 days annual leave per year, in addition to eight bank holidays.
• Relocation package including installation grant.
• Campus life: Free shuttle bus, on-site library, subsidised gym and cafeteria, casual dress code, extensive sports and social club activities.
• Family benefits: On-site nursery, child sick leave, generous parental leave, holiday clubs, and monthly family and child allowances.
• Contract duration: This position is a 3-year contract.
• Salary: Monthly salary starting at £3,303 - £3,695 after tax plus benefits.
• International applicants: Visa exemptions offered.
• Diversity and inclusion: Encouragement of applications from women, LGBTQ+, and individuals from all nationalities.

Job location: This role is based in Hinxton, near Cambridge, UK. You will be required to relocate if you are based overseas.

To apply, please submit a covering letter and CV via our online system. Applications will close on 04/09/2026.