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Job Description

AI|ffinity s.r.o. is seeking a talented and enthusiastic candidate to join our scientific team as a PhD student. The candidate will begin working on AI|ffinity’s projects one year before starting the official PhD programme in 2026. This preparatory year allows focused development of the necessary skills in programming, Cheminformatics, Deep Learning, Data Analysis, and Modeling (using RDKit, PyTorch, Scikit-Learn, Pandas) as well as familiarity with the company’s software and technology. The official PhD programme includes 4 compulsory courses and state exams. Previous experience has shown that first-year PhD students cannot cope with both studying and company work simultaneously; this preparatory year addresses that issue.

Job Type:

  • Hybrid, full-time (FTE 1.0) with a flexible working schedule.
  • Net salarystarting from 30,000 Kč (gross salary 40,140 Kč), which will be adjusted to the candidate’s skills and qualifications. This salary will increase per semester, commensurate with the candidate’s evolving expertise and professional development.
  • According to the Higher Education Act (ZVŠ) of the Czech Republic all full-time doctoral students in the academic year 2025/2026 must receive a total net salary of at least 24,960 Kč a month.
  • Salary in the last PhD years will reach the postdoc salary in Czech academia (see https://docs.google.com/spreadsheets/d/1Qx2tH_WH7zGOfZMUjM9Ii-rAAis2tle_bz3ImtIcN5U/edit?usp=sharing for reference).
  • Overview of the living costs in Czechia: https://docs.google.com/document/d/1njB5brWJ5U5nIIVKow-XM8SgAzwmtXqAb6wQp3dtcOI/edit?usp=sharing
  • This position is initially for a period of 5 years (1 preparatory year + 4 years in the PhD programme), with the possibility of extension.
  • The student will be based at the University of Chemistry and Technology in Prague, as well as the premises of AI|ffinity s.r.o. in Prague.
  • The study program is in English language.
  • The official application deadline for the PhD programme is on the 15th of April 2026, however the ideal candidate can commence work on the project immediately on an employment contract with AI|ffinity.

About the Host Institutions:

Founded in late 2021, AI|ffinity s.r.o. is a Masaryk University spin-off, supported by the Central European Institute of Technology (CEITEC) in Brno. We specialize in leveraging NMR, AI, and Cheminformatics to innovate in the pharmaceutical and biotechnology sectors. With headquarters in Brno, Czech Republic, and premises in Prague, we are at the forefront of scientific advancement. Learn more at www.aiffinity.com.

The University of Chemistry and Technology, Prague, stands as a prestigious institution in the field of chemical sciences. Renowned for its rigorous academic programs and cutting-edge research, the university fosters an environment of innovation and excellence. Its commitment to integrating theoretical knowledge with practical applications makes it an ideal partner for initiatives at the forefront of Cheminformatics and AI-driven drug discovery.

Responsibilities:

The successful candidate will be an integral part of a dynamic, multidisciplinary team at the intersection of Cheminformatics, Artificial Intelligence, and NMR for innovative drug design. This role involves:

  • Contributing to the development of AI|ffinity’s integrated NMR-AI platform, focusing on virtual screening, hit discovery, and hit-to-lead. This task includes developing innovative software solutions for:
  • Enhancing 2D molecular representation to bolster the accuracy of ligand-based virtual screening, utilizing 1D NMR screening spectra.
  • Improving AI-driven, structure-based hit-to-lead algorithms, harnessing the power of 1D NMR restraints.
  • Innovating in de novo drug design algorithms by leveraging ligand epitope information from 1D NMR screening experiments.
  • 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.
  • Engaging in international collaborations through a minimum one-month internship with one of AI|ffinity’s global partners, gaining invaluable exposure and insights that can be directly applied to ongoing drug discovery initiatives.
  • Completing exams from the Individual Study Plan (ISP), focusing on core bioinformatics and chemoinformatics subjects, while also integrating interdisciplinary knowledge from complementary subjects. This approach ensures a robust theoretical foundation and a holistic understanding, vital for practical applications in drug discovery and the development of new software at the intersection of Cheminformatics and AI.
  • Actively participating in team meetings and consultations with senior scientific advisors to discuss project progress, new developments, and strategize future tasks.
  • Contributing to the scientific community through publication and grant writing, aiming to advance the field and secure funding for future research endeavors.

General Requirements:

  • M.Sc. in Cheminformatics, Bioinformatics, Physical Chemistry or a related field, and B.Sc. in Chemistry, Pharmacy, Informatics, Biochemistry or related field.
  • Knowledge of programming in Python.
  • Experience with UNIX OS.
  • Experience in molecular modeling.
  • Very good command of the English language (B2 level or higher).
  • The following qualifications are not mandatory, but will certainly be advantageous:
  • Previous experience in molecular dynamics simulations.
  • Basic knowledge of NMR.
  • Prior experience in Machine Learning/Deep Learning.
  • Scientific publications.
  • Contributions to open source code on GitHub.
  • 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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