Computational Biologist / Bioinformatician - Chemical Biology Services

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.

Project Overview

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. Your work will involve developing descriptors to characterise the binding site of proteins in terms of their ability to recognise ligands, and using these descriptors to assess druggability of protein binding sites.

Responsibilities

• Develop descriptors to characterise protein binding sites and assess their druggability.
• Use AI based and classical machine learning methods to identify endogenous ligands.
• Work closely with structural biology, cheminformatics, and AI teams at UCL and EMBL EBI.
• Support functional annotation of proteins through molecular docking, virtual screening, and calculation of chemical properties.

Required Qualifications

• 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 characterising binding sites and assessing druggability.
• Strong foundation in cheminformatics, including analysis of molecular representations, chemical similarity, fingerprint design, and clustering techniques.
• Experience with molecular docking, virtual screening pipelines, and calculation of chemical properties to support functional annotation.
• Proficiency in Python and 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 with structured collaborative software development 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.
• Advanced English language skills.

Preferred Experience

• Experience using PyMOL or other 3D molecular visualization tools (ChimeraX, VMD) for detailed analysis of protein surfaces and binding pockets.
• Experience in scripting within visualization software to automate the generation of structural descriptors.
• Experience with AI based methods such as Geometric Deep Learning, Graph Neural Networks, or LLMs for structural data processing.

Salary and Contract

Salary: Grade 5 or 6 depending on experience, from £3,303.40 or £3,695.61 after tax plus generous benefits (excluding personal pension and insurance contributions). Contract length: 3 years grant limited, with the possibility to extend for a further year.

Benefits

• 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 - hybrid patterns.
• Private medical insurance for you and your immediate family (including prescriptions and generous dental & optical cover).
• 30 days annual leave per year, plus public holidays.
• Relocation package including installation grant (if required).
• Campus life: free shuttle bus to and from work, on site library, subsidised gym and cafeteria, casual dress code, extensive sports and social club activities (on campus and remotely).
• On site nursery, 10 days of child sick leave, generous parental leave, holiday clubs on campus and monthly family and child allowances.
• 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.

Equal Employment Opportunity

We are committed to ensuring our employees feel valued, supported and empowered to reach their professional potential. Diversity and inclusion: At EMBL, we believe diverse teams drive innovation and scientific excellence. We encourage applications from candidates of all genders, identities, nationalities and other diverse backgrounds. EMBL is a signatory of DORA. Find out how we apply DORA principles to our recruitment and performance assessment processes here.