Bioinformatician – Structural Proteomics & Integrative Modelling

1000 European Molecular Biology Laboratory; Hinxton; Hybrid; GBP 55,000 - 75,000; Full time

Benefits offered by this job

Hybrid working patterns

Private medical insurance

30 days annual leave

Relocation package

Job summary

EMBL-EBI is seeking a Bioinformatician to join the Velankar team within PDBe to advance standards and infrastructure connecting XL-MS, CF-MS and integrative models with proteomics data and structural biology formats.

You will develop interoperable software tools, validation workflows and data deposition pipelines, collaborating with international partners to enhance data interoperability, provenance and reuse across resources.

Qualifications

• PhD in Bioinformatics, Computational Biology, Structural Biology, Proteomics, Computer Science or a related field.

Responsibilities

• Analyze current XL-MS, CF-MS, AP-MS and integrative modelling workflows to define data and metadata requirements.
• Contribute to the extension and adoption of community standards for structural interactomics and integrative modelling data.
• Develop data models and interoperable software tools that connect proteomics and structural biology formats, including suitable conversion of proteomics outputs into integrative modelling representations.
• Develop and maintain tools, APIs, workflows and documentation that support standard-compliant data deposition and local validation.
• Implement approaches for cross-modality validation, identifier mapping and provenance tracking between experimental evidence, structural restraints and integrative models.
• Work with PRIDE and PDB-IHM colleagues to establish linked deposition, release and access workflows across relevant resources.
• Contribute to integrated search, visualisation and programmatic access services for structural interactomics data.
• Engage with researchers, analysis-tool developers and standards communities to support testing, adoption and further development of the infrastructure.
• Contribute to scientific publications, technical documentation, training and dissemination activities.

Skills

Python

Linux

REST APIs

Data integration

FAIR data principles

Education

PhD in Bioinformatics/Structural Biology/Proteomics

Tools

Git

Docker

Kubernetes

Job description

About the team/job

We are seeking a Bioinformatician with expertise in structural biology, proteomics and integrative/hybrid structure modelling 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 maintain the global archive of experimentally determined macromolecular structures, the Protein Data Bank (PDB). We also manage the community-led PDBe Knowledge Base (PDBe-KB) and the AlphaFold Protein Structure Database (AFDB), a collaboration with Google DeepMind. The team brings together scientists, software engineers and data engineers to develop tools and services for structure deposition, data integration, advanced search and biological interpretation. This is an exciting opportunity to develop FAIR infrastructure for structural interactomics and integrative/hybrid modelling. The project will connect experimental proteomics evidence, including crosslinking mass spectrometry (XL-MS), co-fractionation mass spectrometry (CF-MS) and affinity-purification mass spectrometry (AP-MS), with structural restraints, predicted structures, integrative models and molecular interaction data. Working in close partnership with colleagues in PRIDE and wwPDB, you will help establish the data standards, deposition workflows, validation approaches and access services needed to make these interconnected datasets discoverable, interpretable and reusable. The role is ideal for a scientist who enjoys working across disciplines and wants to make a lasting contribution to open scientific infrastructure.

Your role

You will contribute to the development of standards and infrastructure that connect structural interactomics experiments, proteomics evidence and integrative structure models. You will work at the interface of structural biology, proteomics and scientific software development, applying both biological understanding and technical expertise to improve the interoperability, provenance and reuse of these data. A central component of the role will be developing practical approaches for representing experimental context and linking evidence across repositories to streamline data deposition. You will contribute to the extension and adoption of established community standards, including those for proteomics metadata and identifications, and develop tools that support the conversion, validation and deposition of standard-compliant data. You will work closely with international collaborators, community standards organisations, data-resource providers and developers of analysis tools. The resulting infrastructure will enable researchers to move transparently from proteomics evidence and structural restraints to integrative models, molecular interactions and biological annotation.

Your main responsibilities will include:

• Analyse current XL-MS, CF-MS, AP-MS and integrative modelling workflows to define data and metadata requirements.
• Contribute to the extension and adoption of community standards for structural interactomics and integrative modelling data.
• Develop data models and interoperable software tools that connect proteomics and structural biology formats, including suitable conversion of proteomics outputs into integrative modelling representations.
• Develop and maintain tools, APIs, workflows and documentation that support standard-compliant data deposition and local validation.
• Implement approaches for cross-modality validation, identifier mapping and provenance tracking between experimental evidence, structural restraints and integrative models.
• Work with PRIDE and PDB-IHM colleagues to establish linked deposition, release and access workflows across relevant resources.
• Contribute to integrated search, visualisation and programmatic access services for structural interactomics data.
• Engage with researchers, analysis-tool developers and standards communities to support testing, adoption and further development of the infrastructure.
• Contribute to scientific publications, technical documentation, training and dissemination activities.

Qualifications

• You have PhD in Bioinformatics, Computational Biology, Structural Biology, Proteomics, Computer Science or a related field.
• Familiarity with structural biology, protein structure or molecular interaction data.
• Experience working with biological data, metadata, identifiers and scientific repositories.
• Understanding of sequence, structure and functional annotations of proteins.
• Experience in scientific software development, preferably using Python.
• Experience designing or implementing data-integration workflows, APIs or data-processing pipelines.
• Familiarity with FAIR data principles, metadata standards and reproducible research practices.
• Experience with Linux environments, Git, testing and documentation practices.
• Scientific publications relevant to structural biology, bioinformatics, proteomics or biological data resources.
• Strong communication, collaboration and problem-solving skills.
• You might also have Familiarity with integrative/hybrid modelling, structure prediction or macromolecular modelling.
• Experience with mass-spectrometry-based proteomics, particularly XL-MS, CF-MS or AP-MS.
• Experience with community data standards, such as IHMCIF, mmCIF, mzIdentML, SDRF-Proteomics.
• Experience developing data validators, conversion tools, deposition systems or scientific web services.
• Familiarity with REST APIs, databases, containerisation technologies or workflow-management systems.
• Experience in data visualisation and analysis.
• Experience using AI-assisted coding tools responsibly, with appropriate testing, code review, documentation and validation.
• Experience working in international and interdisciplinary teams.
• Experience reporting and presenting scientific topics.

Contract length: 3 years fixed-term (grant based contract) Salary: Grade 5 or Grade 6, salary from £3,452 or £3,861 after tax, plus generous benefits and financial allowances based on individual circumstances. Excluding 12.99% personal pension and insurance contributions.

Interviews: Initial interviews via Zoom are expected to take place in November 2026. Further details will be provided to shortlisted candidates.

Why join us

Do something meaningful

At EMBL-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.

Watch this video to see how EMBL-EBI makes an impact.

Enjoy lots of benefits

• Financial incentives: Monthly family, child and non-resident allowances, annual salary review, pension scheme, death benefit, long-term care, accident-at-work and unemployment insurances
• Flexible working arrangements - including hybrid working patterns
• 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 public 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

What else you need to know

International applicants: We recruit internationally and successful candidates are offered visa exemptions. Please take a look at our International Applicants page for further information.

EMBL is a signatory of DORA. Find out how we apply DORA principles to our recruitment and performance assessment processes here.

Diversity and inclusion

At EMBL, we believe that diverse teams drive innovation and scientific excellence. We encourage applications from candidates of all genders, identities, nationalities and/or any other diverse backgrounds.