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Job Description

AI|ffinity s.r.o. is seeking a talented and enthusiastic Structural Bioinformatics – NMR developer to join our scientific team. We are developing an integrated NMR-AI platform that will reshape the structural biology landscape. Please no recruiters or agencies.

Job Type:

  • Hybrid or remote, full-time position (FTE 1.0) with a flexible working schedule.
  • Residency in Czechia is preferred but for exceptional candidates residence in any EU country could be considered.
  • Offered as an employment contract but for exceptional candidates a consultant contract could be considered.
  • Gross salary starting from 60,000 Kč, will be adjusted based on the candidate’s skills and qualifications.
  • Saraly is adjusted according to the living costs in Czechia (see https://docs.google.com/document/d/1njB5brWJ5U5nIIVKow-XM8SgAzwmtXqAb6wQp3dtcOI/edit?usp=sharing) but for exceptional candidates living in other EU countries a higher salary could be considered.
  • Salary is above the average for postdocs and research associates in Czech academia (see https://docs.google.com/spreadsheets/d/1Qx2tH_WH7zGOfZMUjM9Ii-rAAis2tle_bz3ImtIcN5U/edit?usp=sharing for reference).
  • Annual salary increases commensurate with the candidate’s evolving expertise and professional development
  • This position is initially offered for one year. Upon mutual satisfaction, it may be extended to an indefinite term.

About the Company:

AI|ffinity was founded in late 2021 as a spin-off of Masaryk University, with support from the Central European Institute of Technology (CEITEC) in Brno. The company has developed a unique technology platform that integrates NMR, AI, and Cheminformatics to advance structural biology, drug discovery and protein engineering. The company excels in structure determination of dynamic proteins, hit discovery and hit-to-lead processes, with a strong focus on the structural characterization and mapping of protein-molecule interactions. By leveraging 1D NMR data, AI|ffinity characterizes protein-ligand interactions, enabling the discovery and optimization of new binders. This innovative NMR-AI platform not only accelerates drug discovery but also enhances success rates and reduces costs. On the structure determination front, AI|ffinity’s NMR-AI platform employs special 3D, 4D and 5D NMR experiments together with AI algorithms that expand the size limits of NMR, making the technology ideally suitable for proteins > 20 kDa and intrinsically disordered proteins. With headquarters in Brno, Czech Republic, and additional facilities in Prague, AI|ffinity stands at the forefront of scientific innovation. Learn more at www.aiffinity.com.

Responsibilities:

The successful candidate will be an integral part of a multidisciplinary team solving problems at the intersection of Artificial Intelligence, Structural Bioinformatics and Protein NMR for innovative Drug Design. This role involves:

  • Contributing to the development of AI|ffinity’s integrated NMR-AI platform, with a focus on protein(-ligand) structure determination. This task includes:
  • Enhancing AI|ffinity’s 4D-GRAPHS software for automated chemical shift assignment,
  • Adapting transformer-based deep learning models for protein structure prediction (e.g., OpenFold, Chai-1, Boltz-1) to incorporate experimental restraints from NMR, SAXS, and Cryo-EM.
  • Establish enhanced sampling molecular dynamics protocols for 3D structure ensemble generation using restraints from NMR, SAXS and Cryo-EM experiments. For an overview of this technology, watch our YouTube videos: https://www.youtube.com/@ai-ffinity965/videos
  • Providing computational and modeling support for drug discovery and protein engineering projects by applying AI|ffinity’s NMR-AI platform in collaboration with industrial and academic partners.
  • Enhance AI|ffinity’s SaaS platform by developing and integrating new features.
  • Assisting in the management and maintenance of the company’s IT infrastructure, including PCs, computer clusters, and cloud environments.
  • Participating actively in team meetings and consultations with senior scientific advisors to discuss project progress, explore new developments, and strategize future tasks to achieve company and client objectives.
  • Help in mentoring of PhD students.
  • Contributing to publication and grant writing.

General Requirements:

  • PhD in Biophysics, Structural Bioinformatics, Computational Chemistry, Molecular Modelling, or a closely related field with solid background in protein structure prediction.
  • Experience with UNIX OS.
  • Strong programming skills in Python, with expertise in libraries for data analysis (pandas) and machine learning (scikit-learn).
  • Proven experience in developing deep learning software and proficiency with frameworks such as TensorFlow or PyTorch.
  • Knowledge of version control systems (e.g., Git and GitHub) and high-performance computing infrastructure.
  • Extensive practical experience in protein structure prediction and molecular dynamics simulations of protein-ligand systems.
  • Basic knowledge of NMR will certainly be advantageous.
  • Proven track record of publishing relevant research in peer-reviewed journals, conferences, or code contributions to open-source projects.
  • Very good command of the English language (C1 level or higher).
  • Strong communication skills with the ability to effectively collaborate within multidisciplinary scientific teams.
  • Capable of managing multiple projects concurrently and adept at shifting focus between them in line with the company’s evolving priorities.
  • A strong team player with enthusiasm, a positive attitude, creativity, and a great sense of humor!

Application Process:

  • Candidates are requested to provide two letters of recommendation from previous employers, which should be sent directly to Thomas Evangelidis at tevang@aiffinity.com. Along with these, applicants should include a letter of intent detailing their reasons for applying for this position, as well as a link to their GitHub account showcasing any previous open-source projects, if available.

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