Computational Biologist​/Bioinformatician - Chemical Biology Services

Position: 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. 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 Git Hub/Git Lab. 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 (Chimera

X, 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…