Ph.D scholarship in silico models for assessment of the allergenic potential of food proteins

ESR 1: Ph.D scholarship in silico models for assessment of the allergenic potential of food proteins

Host organisation: Drug Design and Bioinformatics Lab, Faculty of Pharmacy, Medical University of Sofia

Recruited education level: Academic, Master degree

Area/topic: Food Allergy, allergenicity models, prediction toolbox, novel food safety, allergy sensitisation, routes of sensitization

Position: PhD Candidate – MSCA fellow part of MSCA-DN project ALLPreT - No 101072377

Application deadline: 28 November 2022

Planned start date: May 2023

Do you want to contribute to developing new tools for predicting allergenicity of novel foods and alternative food proteins and enable the production of new and safe food for the future?

If you have knowledge within the area of allergy and immunology as well as experience working with in vivo models and are looking for a PhD fellowship opportunity to put your skills into practise, you have it right here. The medical University of Sofia  is looking to recruit a talented and highly motivated PhD student for one of 10 PhD fellowship positions being part of the ALLPreT project. The ALLPreT project is an international European Union’s Horizon Europe research and innovation programme funded Marie Skłodowska-Curie Doctoral-Network project (ALLPreT - No 101072377)

As part of the ALLPreT project and as our new colleague Medical University of Sofia, you will be part of dynamic and highly ambitious research and innovation environments with many national and international collaborators from both academia and industries.

Project description

The allergic response to food proteins follows the mechanisms of the immune system to deal with foreign proteins. Recent approaches for assessment of the allergenic potential of a protein do not allow the prediction of its sensitisation and cross-reactivity potential. In ESR project 1 we will use ligand-based and structure-based approaches to develop in silico models for each of the main stages of the process of transformation of a protein into peptides with allergenic potential. Data of allergens with clinical manifestations will be provided by ERS2. We will validate the derived models with data obtained from in vitro and in vivo studies (ESR3-10).

Responsibilities and tasks

For this project, we seek a highly motivated biomedical scientist/immunologist or equivalent background to develop new predictive in silico tools for the assessment of sensitisation and cross-reactivity. The ESR will collect data and apply molecular docking, quantity structure-activity relationship (QSAR) approaches, and machine learning techniques to model different stages of the sensitisation phase, such as digestion, lysosomal degradation, and binding of peptides to human leukocyte antigen (HLA) proteins. The derived models will be validated with legume reference proteins. The ESR will be involved in the step-by-step development of an in silico model.


We are looking for a team player with the motivation and drive needed for making a difference that matters. You should have a critical mindset, be curious and eager to learn. As you will join international teams, a good command of written and spoken English is necessary.

Your CV comprises a Master’s degree (or equivalent) in biomedical sciences, immunology or a related field with the average marks on both levels of study equivalent or above 8 (scale 6-10);  as well as:

  • Preferably programming experience (Python, R) and/or familiarity with the molecular docking ;

According to the rules for MSCA doctoral networks, applicants should not have resided or worked in Bulgaria for more than 12 out of the last 36 months.

We offer

  • A position part of an innovative and international EU funded Marie Skłodowska-Curie Doctoral-Network (project ALLPreT - No 101072377)
  • Temporary contract for 3 years, Full time position.
  • Full access to the training scheme offered within the ALLPreT project including the development of technical and soft skills (e.g., networking, organization of meetings, grant writing, work/private balance and presenting for different audiences).
  • External stays, including two secondments are a mandatory part of your new PhD fellowship position, where Pioneer Hi-Bred International (USA), for 6 months, to learn how to work with advanced biostatistics tools and models for the risk assessment of genetic modified proteins within a scientific commercial environment, will be the hosting institute.

Terms of Employment: Temporary contract, 3 years position, a full time position (40h/week). Your gross salary will be in line with the collective labour agreement of the Medical University of Sofia and Compensation package will comply with the MSCA-ITN programme regulations for early stage researchers (ESR), which will be approximately 1863 EUR for living allowance, 600 EUR mobility allowance and if applicable family allowance of 495 EUR per month.

Information on the host organization and department:

The Medical University of Sofia (MUS) is the oldest medical institution of higher education in Bulgaria. The Faculty of Pharmacy is one of the four Faculties (campuses) of the MUS. The Drug Design and Bioinformatics Lab (DDBL, is located at the Faculty of Pharmacy. The main areas of expertise at the DDBL are physical and colloid chemistry, drug design, and pharmacokinetics. The research activities of DDBL include in silico immunogenicity and allergenicity modelling and prediction, and IT-based design of novel drugs. Our models and databases are implemented on freely available and widely used web servers for antigenicity prediction (VaxiJen), immunogenicity prediction (EpiDOCK, EpiTOP), allergenicity prediction (AllerTOP, AllergenFP, AllerScreener). The research facilities of DDBL include 4 high-performance computing servers and software for molecular modelling, docking and QSAR.

For further information: Prof. Ivan Dimitrov:

Application procedure uitklapper, klik om te openen

Candidates can apply for a position using the 'apply now' button

Your complete online application must be submitted no later than 28 November, 2022.

Applications must be submitted as one PDF file containing all materials to be given consideration. To apply, please use the apply now button, fill out the online application form, and attach all your materials in English in one PDF file. The file must include:

  • A letter motivating the application (cover letter)
  • Curriculum vitae

You may apply before obtai­ning your master's degree but cannot begin before having received it.

Applications received after the deadline will not be considered.

All interested candidates irrespective of age, gender, race, disability, religion or ethnic background are encouraged to apply.

Please note, candidates can apply to max two ESR positions.

Information on the ALLPreT project

Introducing novel foods, such as insects, will strongly contribute to the security and stainability of our food supply. However, these novel foods must be safe (EU regulation 2015/2283). Allergenicity assessment is an essential part of the safety assessment of novel foods. Unfortunately, current methods to assess de novo allergenicity lack predictive power and are not validated. Consequently, food producers and risk assessors struggle with allergenicity assessment, slowing the introduction of novel foods into our food supply. Enabling the safe introduction of novel foods while protecting humans from unacceptable food allergy risks calls for a multidisciplinary approach. The ALLPreT consortium is a highly multidisciplinary group of experts from universities, research institutes, hospitals, patient organisations, and industry arising from the EU COST Action ImpARAS (Improved Allergenicity Risk Assessment Strategy). This puts them in an ideal position to consolidate their previous collaboration and establish an innovative doctoral training network in this area. The overall goal of ALLPreT is to train the next generation of scientists who can tackle the shortcomings in the current food allergy assessment of novel food products. ALLPreT will train 10 PhD students in the core aspects of food allergy risk assessment, immunology, protein chemistry, bioinformatics, in vitro/in vivo/in silico model development and complementary “soft” skills to deliver well-educated young scientists, with a unique position within the EU labour market. The PhD students will explore the new field of research on de novo sensitisation by novel foods and develop a toolbox of in vitro/in vivo/in silico allergenicity prediction tools that are scientifically sound, validated, and easily usable by industry and food safety authorities. This toolbox will contribute to fast and accurate safety assessment, thereby speeding up safety approval and market uptake of novel foods. Read more at

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