We are looking for a highly motivated Computational Biologist / Bioinformatician to join the Chemical Biology Resources team at the European Bioinformatics Institute (EMBL-EBI), located on the Wellcome Genome Campus near Cambridge, as part of the Wellcome Trust funded LIGMAP project, a multi-disciplinary collaboration between University College London and EMBL-EBI.
The Chemical Biology Resources team provides world-leading chemogenomics resources to the scientific community. ChEMBL is a database of quantitative small-molecule bioactivity data curated primarily from the scientific literature widely used to support drug discovery projects in industry and academia. ChEBI is a highly curated database and ontology of compounds of biological interest.
The EBI is part of the European Molecular Biology Laboratory (EMBL) and it is a world-leading bioinformatics centre providing biological data to the scientific community with expertise in data storage, analysis and representation. EMBL-EBI provides freely available data from life science experiments, performs basic research in computational biology and offers an extensive user training programme, supporting researchers in academic and industry.
Your role
LIGMAP is an ambitious 4.5 year project, led by University College London, to identify the endogenous ligands of the many proteins of unknown function in the proteome using AI-based methods as well as classical machine learning. You will work closely with the PDBe team at EMBL-EBI, as well as leading researchers in structural biology and machine learning at University College London, to deliver the goals of the project. You will develop descriptors to characterise the binding site of proteins in terms of their ability to recognise ligands, and use these to assess druggability of protein binding sites.
You have:
A PhD in Bioinformatics, Structural Biology, Chemistry, Computer Science, or a related field.
Deep understanding of protein-ligand interactions and expertise in protein structure analysis, specifically in characterizing binding sites and assessing druggability.
Strong foundation in cheminformatics, including analysis of molecular representations, chemical similarity, fingerprints design, and clustering techniques, among others.
Experience with molecular docking, virtual screening pipelines, and the calculation of chemical properties to support functional annotation.
Proficiency in Python, with hands-on experience using cheminformatics and structural biology libraries such as RDKit, Biopython, or Open Babel.
Familiarity with structural data formats (mmCIF, PDB) and experience working with global resources like the Protein Data Bank (PDBe).
Experience working with relational (SQL) databases and managing large-scale biological or chemical datasets.
Familiarity working in a structured collaborative software development environment using git and GitHub/GitLab.
Proficiency in working with Linux operating systems.
Self-motivated with a can-do attitude and a willingness to solve complex problems in a multi-disciplinary team.
Excellent communication and interpersonal skills, with the ambition to work effectively with international collaborators across institutions like EMBL-EBI and UCL.
Advanced English language skills.
You might have:
Experience using PyMOL or other 3D molecular visualization tools (ChimeraX, VMD) for the detailed analysis of protein surfaces and binding pockets
Experience in scripting within visualization software to automate the generation of structural descriptors.
Experience in using AI-based methods, such as Geometric Deep Learning, Graph Neural Networks, or LLMs for structural data processing.
Salary : Grade 5 or 6 depending on experience. Salary from £3,303.40 or £3,695.61 after tax plus generous benefits. Excluding personal pension and insurance contributions.
Apply now! Benefits and Contract Information
Financial incentives: depending on circumstances, monthly family/marriage allowance of £278 monthly child allowance of £336 per child. Non resident allowance up to £569 per month. Annual salary review, pension scheme, death benefit, long-term care, accident-at-work and unemployment insurances
Hybrid 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 (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 allowances
Contract duration: This position is a 3 year contract.
Salary: Monthly salary starting from £3,303.40 or £3,695.61 (depending on experience) after tax plus generous benefits. Excluding personal pension and insurance contributions.
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.
How to apply: To apply please submit a cover letter and a CV through our online system before the closing date.
To apply, please submit a covering letter and CV via our online system. Applications will close on 17/06/2026.
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