Peptide Design Team Lead (W/M)

Micropep is building a more sustainable agriculture for future generations. We develop natural crop protection solutions based on the incredible potential of micropeptides, small, naturally occurring protein molecules that target and regulate plant genes and proteins. We are building the next generation of sustainable solutions for farmers who care about their crops and the future of our planet.

Micropep was founded in 2016 as a spin-off from the “LRSV”, a French plant research laboratory of the French National Centre for Scientific Research (CNRS) and the University of Toulouse, an AgriTech center of excellence. To date, Micropep has raised nearly $60 million from leading European and U.S. investors and began its expansion to the United States in 2022.

We are a team of more than 50 accomplished and driven people from a wide range of scientific, technical, and business backgrounds. We are united by our desire to make a positive impact on our planet. Together, we are revolutionizing crop protection through our proprietary micropeptide technology.

You will join an interdisciplinary R&D team where Artificial Intelligence is the central engine of our active-molecule discovery.

ESSENTIAL DUTIES & RESPONSIBILITIES

You will be in charge of the “Peptide Design & Target” team. Your team is responsible for:

• target selection and characterization for peptide design;
• designing peptides for screening;
• leveraging AI to accelerate lead identification;
• performing continuous learning (DMTA cycle/Design-Test-Learn loop) to improve the performance of designs and prediction models.

You will be responsible for team management and peptide design:

Team leadership

• Oversee the management of AI experts, chemo-computer scientists, bioinformaticians, ensuring their work aligns with project objectives and timelines.
• Maintaining a scientific and technical watch and staying abreast of the state-of-the-art in the fields of protein structure prediction and peptide and protein design, from both global research and industrial perspectives.
• Define roadmaps
• Foster a culture of data-driven decision-making within the team
• Accountable for the delivery of the work on time in full and with high-quality standards.
• Ensure efficient communication with peers and Project Management Office
• Contribute proactively to Innovation and Research & Development projects
• Ensure alignment between personal development and business needs
• Implementation of OKRs and KPIs tracking
• Conduct performance reviews
• Define and follow budget
• Design and optimization of peptide candidates using advanced computational biology and AI techniques
• Provide state-of-the-art methodologies and capabilities for peptide design and optimization, peptide/protein interaction prediction, applying bio/chemoinformatics techniques, latest machine learning algorithms
• Work with your AI experts to guide the development of ML/DL models
• Identify and propose relevant targets, in collaboration with other scientific teams
• Characterize and validate these targets for peptide design
• Active watch in AI, design…
• Designing, developing, building, and maintaining peptide design pipelines, focusing on (but not restricted to) structural and conformational aspects.
• Performing structural analyses of systems of interest (detection of pockets, detailed analysis of protein/protein interfaces, docking pose, etc.)
• Engage with other peptide and protein design companies to develop partnerships or to conduct joint projects.

QUALIFICATIONS & EXPERIENCE

Required:

• Ph.D. in computational chemistry, molecular modeling, structural biology, machine learning, or a related field, with a strong theoretical background as demonstrated by contributions to leading journals; or an equivalent combination of education and experience.
• At least 3 years of hands‑on experience (industry preferred) in peptide / protein‑peptide interaction (PPI) design, structure‑based drug/biologics discovery, or closely related computational biology.
• Demonstrated expertise with modern protein structure prediction and design tools, including AlphaFold / AF‑Multimer, ProteinMPNN, RFdiffusion, BindCraft, BoltzGen, Rosetta, and physics‑based peptide docking (e.g. AutoDock CrankPep). Ability to critically evaluate, benchmark and integrate new tools as the field evolves.
• Strong knowledge of DL/ML(embbedings, transfer learning, ...) and other methods (QSAR...).
• Strong working knowledge of molecular modeling techniques: docking, molecular dynamics & enhanced sampling, homology modeling, virtual screening, structure- and ligand-based design.
• Excellent scientific programming skills (Python required; familiarity with HPC / GPU workflows). Comfortable using AI‑assisted coding tools (Copilot, Cursor, Claude Code, etc.).
• Experience working with AWS (EC2, lambda, GPU...) is highly appreciated.
• Ability to carry out in‑depth analysis, present results and conclusions to scientists and non‑scientists (management team, board of directors...).
• Strong knowledge of DL/ML(embbedings, transfer learning, ...) and other methods (QSAR...)
• Demonstrated ability to work successfully in cross‑functional and third‑party teams, emphasizing teamwork, collaboration and communication.
• Good communication skills, both written and oral (English mandatory), especially with non‑experts.
• Thoroughness, attention to detail, and pragmatism.
• Good organizational skills and ability to optimize the work environment (processes, procedures, etc.).
• High level of self‑motivation, intellectual curiosity, and eagerness to thrive in a fast‑paced, multidisciplinary, and team‑oriented start‑up environment.
• Ability to manage multiple projects with overlapping deadlines.
• Natural ability for problem‑solving.

Preferred:

• Experience working with flexible systems (linkers, short peptides, IDPs) is highly appreciated.
• Experience using PyMOL or Chimera is preferred.
• Listening comprehension in French is a plus but not required.

CONDITIONS

• Permanent contract
• Based at Auzeville-Tolosane (Toulouse Area, France) with partial homeworking (2 days)