Research Engineer Intern, Deep Learning for protein structure modelling

InstaDeep, founded in 2014, is a pioneering AI company at the forefront of innovation. With strategic offices in major cities worldwide, including London, Paris, Berlin, Tunis, Kigali, Cape Town, Boston, and San Francisco, InstaDeep collaborates with giants like Google DeepMind and prestigious educational institutions like MIT, Stanford, Oxford, UCL, and Imperial College London. We are a Google Cloud Partner and a select NVIDIA Elite Service Delivery Partner. We have been listed among notable players in AI, fast-growing companies, and Europe's 1000 fastest-growing companies in 2022 by Statista and the Financial Times. Our recent acquisition by BioNTech has further solidified our commitment to leading the industry.
Join us to be a part of the AI revolution!
At InstaDeep’s BioAI department, we push the boundaries of healthcare and medical science by combining cutting-edge biology and artificial intelligence expertise. Our projects range from designing next-generation vaccines and cancer treatments to advancing biopharmaceuticals for infectious disease prevention and therapy. By joining us, you’ll have the opportunity to collaborate with leading scientists, engineers, and biologists from both InstaDeep and BioNTech to tackle critical challenges in medicine.
As a Research Engineer Intern, you’ll work closely with a dynamic team of research engineers and computational biologists. Your mission will be to design innovative approaches for molecular modelling, protein interactions, protein design, and other related areas by leveraging your technical, analytical, and research expertise. You’ll gain a deep understanding of bioinformatics and business challenges while staying updated on the latest advancements in machine learning and biology.

In This Role, You’Ll:

• Identify and apply state-of-the-art technologies to solve complex problems and improve existing solutions.
• Collaborate with a multi-disciplinary team to experiment with diverse approaches, analyse results, and deliver proof of concepts and minimum viable products.
• Ensure continuous improvement and maintenance of industrial-grade solutions.
• Write high-quality, maintainable, well-documented, and modular software libraries.
• This internship sits at the intersection of deep scientific research and practical application, aimed at enhancing our cutting-edge biological AI models by incorporating the effects of ions on protein structure, dynamics and function. You will apply your knowledge of biophysical principles, artificial intelligence, and computational biology to build more physically realistic and predictive tools that accelerate the development of medical treatments.
• Keywords:
• Structural Biology, Biophysics, Computational Chemistry, Protein Structure, Protein Dynamics, Ion–Protein Interactions, Artificial Intelligence, Machine Learning, Drug Discovery, Deep Learning.

Responsibilities:

• Design, implement, and evaluate proof-of-concept methods and benchmarking experiments to explicitly incorporate ion effects into diffusion-based protein structure prediction models.
• Leverage both classical computational biology tools and modern deep learning approaches to predict and analyze ion-induced protein conformational changes..
• Enhance the understanding of AI model behavior by performing rigorous validation against experimental crystallographic and biochemical data, and quantifying performance gains over ion-agnostic models.
• Create, curate, and manage a high-quality benchmark dataset of ion-bound and ion-free protein structures to train and validate predictive models.
• Contribute to and help shape the long-term research for AI-driven therapeutic and peptide design by establishing a physically accurate basis for modeling protein-ligand interactions and allosteric effects of ions.

Requirements

• Strong background in Structural Biology, Computational Biology, Artificial Intelligence, or a related field. A PhD in one of these disciplines, or equivalent experience, is highly valued. A Masters degree is required. 
• Strong programming skills, especially in Python, with hands-on experience using deep learning frameworks such as PyTorch or similar libraries. Experience with Jax is a bonus.
• Proven experience applying classical and/or deep learning algorithms to biological problems, ideally in domains such as protein structure prediction, molecular modeling, or drug discovery. Familiarity with diffusion is a plus.
• Strong foundation in biochemistry/biophysics, with a clear understanding of structure-function relationships of macromolecules.
• Demonstrated ability to design and execute computational experiments efficiently, and to analyze, interpret, and clearly communicate results to a technical audience.
• Excellent communication skills in English.
• Available for 6 months.

Our commitment to our peopleWe empower individuals to celebrate their uniqueness here at InstaDeep. Our team comes from all walks of life, and we’re proud to continue encouraging and supporting applicants from underrepresented groups across the globe. Our commitment to creating an authentic environment comes from our ability to learn and grow from our diversity, and how better to experience this than by joining our team? We operate on a hybrid work model with guidance to work at the office 3 days per week to encourage close collaboration and innovation. We are continuing to review the situation with the well-being of InstaDeepers at the forefront of our minds.
Right to work: Please note that you will require the legal right to work without visa sponsorship in the location you are applying for. We do not sponsor work visas.