Bioinformatician

? About the teamWe 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. The PDBe team consists of an international and interdisciplinary group of scientists, software engineers, and data engineers who develop a range of tools and services that support structure deposition, data integration, and advanced search capabilities for structural biologists and the wider life sciences community.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. The project brings together ELIXIR, Instruct-ERIC, EU-OPENSCREEN, HPC centres, AI factories, and pharmaceutical industry partners to develop FAIR, AI-ready infrastructure for structural ensemble data and molecular simulations.Your roleYou will contribute to the development of infrastructure connecting molecular dynamics simulations with structural biology resources and biological knowledge bases. A major component of the role will be developing AI-driven approaches to mine scientific literature and automatically extract experimental and biological metadata to enrich MD datasets. You will develop and extend 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, to facilitate the integration of MD-derived insights across the wider life sciences data ecosystem.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:Design and implement data integration pipelines that connect MDDB with major life science resources, including PDBe, UniProt, PDBe-KB, and other relevant knowledge bases and databasesDevelop and deploy AI- and machine learning-based approaches for extracting experimental and biological metadata from scientific literature to enrich MDDB datasets and support downstream biological interpretation.Extending and maintaining the SIFTS infrastructure and codebase to support integration of molecular dynamics and other data resourcesDevelop and maintain software tools, APIs, workflows, and documentation that facilitate FAIR data integration, metadata enrichment, and integrated data accessCollaborating with domain experts, software engineers, and data resource providers to enable the integration of MD-derived biological insights into the wider life sciences data ecosystem.Supporting FAIRification, standardisation, and interoperability of MD datasets and associated annotationsCollaborating with international partners across ELIXIR, Instruct-ERIC, EU-OPENSCREEN, HPC centres, and industryParticipating in community standards development, technical documentation, training, outreach, and dissemination activitiesYou havePhD in Bioinformatics, Computational Biology, Structural Biology, Computer Science, Data Science, or a related fieldFamiliarity with structural biology and molecular simulation dataExperience with NLP/LLM-based scientific literature miningDemonstrated experience with FAIR data principles, metadata standards, and scientific repositories.Understanding of sequence, structure, and functional annotations of proteinsExperience in scientific software development, preferably in PythonExperience with Linux environments, Git, and CI/CD practicesScientific publications relevant to structural biology, bioinformatics, or protein annotationsStrong communication, collaboration, and problem-solving skillsYou may also havePostdoctoral research experience in a relevant fieldExperience with graph databases (e.g. Neo4J), REST APIs, containerisation technologies, and workflow management systems such as NextflowExperience in data visualisation and analysisUnderstanding of FAIR data principles and the biological data lifecycleExperience in reporting and presenting scientific topicsExperience working in international and interdisciplinary teamsApply now! Benefits and Contract InformationFinancial incentives: depending on circumstances, monthly family/marriage allowance of £291 monthly child allowance of £351 per child. Non resident allowance up to £595 per month. Annual salary review, pension scheme, death benefit, long-term care, accident-at-work and unemployment insurancesHybrid working arrangementsPrivate 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 holidaysRelocation package including installation grant (as applicable)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, child sick leave, generous parental leave, holiday clubs on campus and monthly family and child allowancesContract duration: This position is a 3 year contractSalary: Monthly salary starting at £3, 303 - £3,695 after tax (but excl. pension & insurances) + benefits (Total package will be dependent on family circumstances)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, near Cambridge, UK. You will be required to relocate if you are based overseas and you will receive a generous relocation package to support you.To apply, please submit a covering letter and CV via our online system. Applications will close on 04/09/2026We will review applications on a rolling basis and in the event that we identify a suitable candidate sooner, we reserve the right to close the vacancy earlier that the published closing dateTPBN1_UKTJ