Overview

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 Masaryk University in Brno, as well as the headquarters of AI|ffinity s.r.o. in Brno.
  • 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 candidate will be enrolled in either the PhD programme at the Faculty of Science, Masaryk University (https://www.sci.muni.cz/en/studies/doctoral-degree-study-programme) or the PhD programme at the Central European Institute of Technology (https://www.ceitec.eu/phd-school/?urltitle=ceitec-phd-school). The specific topic and study programme will be determined jointly by the student and the academic supervisor.

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, focusing on protein(-ligand) structure determination. This task includes developing innovative software solutions for:
  • 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.
  • 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 Biophysics, Structural Bioinformatics, Computational Chemistry, Molecular Modelling, Informatics or a closely related field.
  • Practical experience in protein structure prediction.
  • 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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