Protein Designer/Engineer (Ph.D)

Job description

AI + Biology for sustainable ingredients

SilicoLife is a biotechnology company that harnesses the power of computational biology to sustainably produce valuable compounds through fermentation. Our proprietary technologies and expertise have been utilized by top companies in various industries for over a decade, as well as in research and development projects.

Recently, we received a Series A investment of 9.8 million euros, which will enable us to shift towards becoming a product-focused company. We will now exclusively use our technology and knowledge to create internal intellectual property and products for the high-growth supplements market.

Be part of something extraordinary and join us in our quest.

What’s the job?

As a Protein Design Scientist, you will be a key piece in the development pipeline that we are implementing with the goal of bringing new products to market. You will bring cutting-edge skills in protein modeling and structure predictions to innovate designed solutions enhancing reaction catalysis performance, exploring enzyme promiscuity, cofactor specificity, among other tasks.

The Scientist will join a team of Bioinformatics and Data Scientists working on metabolic engineering, pathway and strain design, genetic construct design, phenotype and genome analysis. Our aim is to improve the performance of microbes via multiple, iterative, rounds of genome engineering. In addition, you will be part of a larger technical team to develop best practices in designing strain edits and computer-aided learning for strain performance.

Job requirements

The successful candidate must have a PhD with 1+ years of experience in bioinformatics, computational biology, biochemistry, biophysics, or related fields

The candidate’s skills and qualifications will ideally include:

  • Strong understanding of protein biochemistry or biophysics related to protein structure/function

  • Demonstrated track record in protein engineering or de novo protein design to achieve an intended goal

  • Experience with molecular modeling workflows such as conformational analysis, docking, binding site assessment, and structural analysis software applications (Rosetta, AutoDock, pyMol, etc.)

  • Proficiency with methods and tools to query and analyze large datasets of public and proprietary sequence and structural data

  • Excellent communication skills and the ability to work in a highly dynamic and collaborative environment

  • Curiosity and willingness to learn new technologies and scientific areas previously unknown to you

Nice to have:

  • Experience working with or evaluating machine / deep learning methods applied to protein prediction tasks. You know of or have worked with, for example: AlphaFold, RoseTTAFold, RFDiffusion.

  • Industry experience in small teams building solutions in the molecular biology domain.

  • Programming experience is a plus.


The selected candidate will work at the interface of the dry and wet lab teams, leading the advancement of functional capabilities in the areas of protein structure, function, in silico engineering and design. Some of your functions will include:

  • Biomolecular modeling: Perform structure and sequence modeling of proteins using software such as Rosetta, molecular dynamics simulations, deep learning, and protein statistical and language models to generate hypotheses and predictions about relationships between protein sequence, structure, dynamics, and function.

  • Model interpretation and application: Understand and predict the effects of sequence variation on protein function and biophysical parameters that are relevant for enzyme and protein engineering and improvement.

  • Streamline workflows: Build computational pipelines to automate routine tasks and develop software to integrate and harmonize large biological datasets from multiple sources for mechanistic interpretation.

  • Present accurate project status to senior leadership, at both a summary and detailed level


Salary will be proposed considering the candidate experience. The selected candidate will be employed by the company and will be part of an interdisciplinary team of experts in computer science, artificial intelligence, bioinformatics, systems biology, molecular biology and bioprocess engineering.

Other benefits also include:

  • Flexible work schedule: great work/life balance

  • Extra vacation days over the 22 legally mandated

  • Participation in internal talks

  • Company retreats

  • Equipped kitchen and free coffee

The selected candidate will be exposed to highly innovative projects combining world-class science with disruptive business models to create sustainable and economically viable solutions addressing global challenges.

SilicoLife is an equal opportunity employer that is committed to creating a diverse and inclusive workplace. We do not discriminate on the basis of race, gender, sexual orientation, religion, age, national origin, disability, or any other protected characteristic. We are dedicated to creating a workplace culture that values diversity, equity, and inclusion and that provides equal opportunities for all employees. We strive to foster a positive and supportive work environment for all, and we believe that everyone should have the opportunity to succeed, regardless of their background or identity. Our policies and practices reflect this commitment, and we are committed to treating all employees with respect and fairness.