Structural Bioinformatics Scientist/Developer
Who We Are
ALLOX is a spin-off of the Centre for Genomic Regulation (CRG) and draws on the expertise and technology developed in the lab of Ben Lehner. The company was born out of the realisation that combining systematic mutagenesis, high-throughput phenotyping and biophysical modelling has the potential to revolutionise drug development but also transform biotechnology in general. In February 2025 we will be relocating to a new incubation space in the Barcelona Science Park (surrounded by 3 research institutes and over 70 different companies), and our immediate goal is to identify allosteric switches in all proteins and then leverage this unprecedented resource to rapidly develop novel medicines to treat human diseases. Our long-term vision is to become a leader in programmable biology, building the next generation of tools to predict, design and engineer new protein functions. We believe in a future where humanity will be able to harness the power of biology to solve our most pressing issues. We are expanding our interdisciplinary team with highly motivated individuals who are excited by this bold vision, share our sense of urgency, but are not willing to compromise on integrity. At ALLOX the success of our revolutionary scientific approach is as important to us as our mission to create a healthy, honest and respectful culture, both internally and with our partners.
For additional information, please visit: https://www.allox.bio/
Who You Are
ALLOX is seeking a talented, enthusiastic and adaptable computational scientist to join our growing startup as a Structural Bioinformatics Developer. You will be an integral part of a multidisciplinary team solving problems at the intersection of Deep Mutational Scanning (DMS), AI and Structural Bioinformatics for Drug Design. Your primary responsibility will be to build out ALLOX’s Structure Engine, key computational infrastructure that will transform the output of the company’s experimental platform into actionable data for the chemistry team and relevant partners. This will involve the following tasks: (1) contextualising ALLOX’s proprietary allosteric maps by integrating them with experimentally determined and computationally predicted protein structures, (2) developing algorithms to identify and prioritize target protein pockets, cryptic sites or surface patches for downstream drug discovery efforts, and (3) leveraging and adapting existing AI tools for de novo protein design to predict peptide binders. The ideal candidate will have a hybrid skill set with domain knowledge in either biophysics, protein engineering or structural bioinformatics as well as strong data science skills and demonstrated experience applying machine learning methods to problems in molecular biology. Regular communication and collaboration with the computational and drug discovery teams will be crucial to identify the highest-impact applications of structural biology data and analyses that align with company goals. This position is therefore ideally suited to an organised, analytical thinker with excellent communication skills and an engineering mindset that recognises the power of structural information in allosteric drug development. If you share our sense of urgency to bring novel and better drugs to address unmet needs and thrive in a fast-paced, multidisciplinary environment, don’t hesitate. Join ALLOX and help us make our mission a reality!
What You'll Do
Software Development
- Lead the development of ALLOX’s Structure Engine, a cloud-based software suite to accelerate the company’s structural biology discoveries.
- Build a pipeline to curate experimental and computationally predicted human protein structures proteome-wide, annotate pockets and calculate druggability estimates.
- Evaluate, adapt and deploy software tools to predict cryptic protein pockets at scale.
- Extract protein structural, physico-chemical features, large language model embeddings and estimates of conformational dynamics (based on MD or other methods) for target proteins.
- Integrate internally-generated/proprietary high-throughput screening data (allosteric maps) with structural models and features to identify potential allosteric mechanisms.
- Develop algorithms to prioritize target protein pockets, cryptic sites or surface patches for downstream drug discovery efforts.
- Stay informed about emerging technologies relevant to the computational platform and explore their potential integration.
Drug Development
- Explore existing AI tools for de novo protein design to predict peptide binders targeting candidate allosteric pockets or sub-domains.
- Contribute to the decision-making process of target selection and pocket prioritisation for drug development.
- Participate in and support drug discovery projects and industry partnerships with domain knowledge and bespoke protein structural analyses.
Communication, Teamwork and Culture
- Establish clear communication channels with the different working teams.
- Keep stakeholders informed about workload, progress, results, and innovations.
- Exemplify best practices and positive behaviours.
- Foster a productive and inclusive working environment.
- Participate in general company duties and contribute to overall success.
Job & Technical Competencies Requirements
- Masters/PhD degree in Biophysics, Protein Engineering, Structural Bioinformatics, Biotechnology, Computational Biology, Computer Science or a related field.
- 5+ years of full-time scientific software development experience (industry or academia).
- Strong knowledge or research experience in the fields of Structural Biology and Biophysics.
- Experience with structural bioinformatics software (e.g., AlphaFold, Rosetta, Gromacs, MODELLER, AutoDock Vina).
- Ability to develop algorithms and apply statistical analysis to structural data.
- Strong programming skills in Python, with proficiency in libraries for structural bioinformatics (Biopython or PyMOL), data analysis (pandas) and machine learning (scikit-learn).
- Experience with UNIX OS and Bash/Shell scripting.
- Knowledge of version control systems (e.g., Git and GitHub) and high-performance computing infrastructure.
- Strong teamwork and collaborative attitude.
- Adaptable, capable of managing multiple projects concurrently and adept at shifting focus between them in line with the company's evolving priorities.
- Strong organisational and record-keeping skills.
- Organised thinker with excellent communication skills, thriving in a multidisciplinary, fast-paced team environment.
- Fluent English.
- Prior experience in a biotech or pharmaceutical company, particularly in drug discovery or development.
- Knowledge of structural biology techniques (X-ray crystallography, NMR spectroscopy, and cryo-EM).
- Practical experience in protein structure prediction and molecular dynamics simulations of protein-ligand systems.
- Experience in developing (geometric) deep learning software and proficiency with frameworks such as TensorFlow or PyTorch.
- Familiarity with cloud-based computing (preferably GCP) environments for handling large datasets and computationally intensive tasks.
- Experience with Docker for packaging and deploying bioinformatics software.
- Proficiency in R and libraries for data science (Tidyverse).
- Fluent Spanish and/or Catalan.
Compensation & Benefits
To determine starting pay, we consider multiple job-related factors including a candidate’s skills, education and experience, the level at which they are actually hired, market demand, business needs, and internal parity. We may also adjust this range in the future based on market data.
This role is eligible for participation in our Annual Performance Bonus Plan (based on company goals by role level and annual company performance) and all employees are offered Equity, subject to the terms of those plans and associated policies.
In addition, ALLOX also provides our employees:
- 25 days annual leave (excluding public holidays)
- Paid parental leave
- Free drinks, snacks and regular team meals
This position is available for full-time on-site work at Barcelona Science Park, a hybrid model combining on-site and remote work, or fully remote work depending on the role and your individual circumstances. We are open to discussing the best option for you during the interview process.
Let’s make programmable biology a reality
The startup nature of ALLOX provides multiple growth opportunities into other areas of the company. As one of the early employees at ALLOX, your work will have a direct impact on the foundation of a groundbreaking new approach to biotechnology.
Application Process
Apply for this job here. The interview process includes a take-home assignment to assess your practical skills.
The closing date for applications is February 28th, 2025. We encourage applicants to submit their application at the earliest opportunity as the closing date may be brought forward if a high volume of applications are received.
*Please note jobs may be taken down from our website, this does not mean they have been filled. This is to maintain our candidate experience for current applicants. If you are in the interview process and would like to request a copy of the job description, reach out to your recruiting contact.

Parc Científic de Barcelona
C/Baldiri Reixac 4-8 (Torre R),
08028 Barcelona
All our switches