PhD student position in AI for life sciences with a focus on protein-ligand interaction dynamics

Are you looking for a PhD position where you develop state-of-the-art machine learning methods for the life sciences (geometric deep learning, transformer-based approaches, ...) with a focus on protein-ligand interaction dynamics in collaboration with wet-lab researchers? If so, this fully funded PhD position might be an excellent match for you.

The interactions and dynamics of proteins and ligands are essential to the biological function of all organisms. For example, haemoglobin must change conformation to bind oxygen and fulfil its biological function. While machine learning approaches that predict the static structure of proteins have become invaluable tools for biologists and medicinal chemists, machine learning-based prediction of protein dynamics is still in its infancy. An additional challenge is the modelling and prediction of the dynamic interaction between proteins and small-molecule ligands, such as hormones, neurotransmitters, or therapeutic drugs. The computational representation of such dynamic interactions between molecules is one of the research lines at the ProbstLab. Beyond introducing new machine learning methodologies and computational representations of molecules, we collaborate with wet-lab researchers to apply the developed methods to problems, including the search for new and potent therapeutics and the development of more sustainable processes to synthesise chemical compounds.

As a PhD student, you will be embedded in a diverse group of international scientists. Your responsibilities and opportunities will encompass:

• Developing new machine learning methodologies that have direct application in the life sciences, focusing on protein-ligand interaction dynamics;
• Following, evaluating, and synthesising state-of-the-art machine learning, chemistry, and biology research, working at the intersection of multiple fields;
• Connecting and collaborating with other national and international researchers in the life sciences and computer science;
• Writing and presenting/publishing research papers at/in internationally renowned conferences/journals. As a group, we aim to publish our work in natural science journals (applications) and at computer science conferences (methods).

You will work here
The Probst Lab (https://probstlab.science) is part of the Wageningen Bioinformatics Chair Group (https://wur.eu/bif). You will be co-supervised by Daniel Probst and Dick de Ridder.

Requirements:

You are a computer scientist, a computational biologist or a computational chemist with proven expertise in implementing machine learning methods in Python. You write or have written your master's thesis on a topic relevant to this project. Proven experience in molecular dynamics simulations of proteins or protein-ligand complexes is an advantage.

You possess:

• A successfully completed MSc degree in computer science or a strongly related field (e.g. computational biology or computational chemistry).
• Proven experience in Python programming or high proficiency in another language such as C/++ or Rust. It is an advantage if you can provide a link to a code repository of a project where you are the main contributor.
• Experience in implementing machine learning methodologies, specifically neural network-based methods, including a mathematical understanding of the methods.
• An interest in applying state-of-the-art machine learning techniques to various fields in the life sciences.
• A collaborative attitude valuing the importance of interdisciplinarity and open science.
• The drive to present and share your work at international conferences and to network with peers at these conferences.
• Excellent English writing skills and experience in scientific writing.

For this position, your command of the English language is expected to be at C1 level. In some cases, it is necessary to submit an internationally recognised Certificate of Proficiency in the English Language. More information can be found here.

Salary Benefits:

Wageningen University & Research offers excellent terms of employment. A few highlights from our Collective Labour Agreement include:

• Partially paid parental leave;
• working hours that can be discussed and arranged so that they allow for the best possible work-life balance;
• the option to accrue additional compensation / holiday hours by working more, up to 40 hours per week;
• there is a strong focus on vitality and you can make use of the sports facilities available on campus for a small fee;
• a fixed December bonus of 8.3%;
• excellent pension scheme.

In addition to these first-rate employee benefits, you will receive a fully funded PhD position and you will be offered a course program tailored to your needs and the research team.
The gross salary for the first year is € 2.901,- per month rising to € 3.707,- in the fourth year in according to the Collective Labour Agreements for Dutch Universities (CAO-NU) (scale P). This is based on a full-time working week of 38 hours. We offer a temporary contract for 18 months which will be extended for the duration of the project if you perform well.

There are plenty of options for personal initiative in a learning environment, and we provide excellent training opportunities. We are offering a unique position in an international environment with a pleasant and open working atmosphere.

You are going to work at the greenest and most innovative campus in Holland, and at a university that has been chosen as the “Best University” in the Netherlands for the 20th consecutive time.

Coming from abroad
Wageningen University & Research is the university and research centre for life sciences. The themes we deal with are relevant to everyone around the world and Wageningen, therefore, has a large international community and a lot to offer to international employees.

Because we expect you to work and live in the Netherlands our team of advisors on Dutch immigration procedures will help you with the visa application procedures for yourself and, if applicable, for your family.
Feeling welcome also has everything to do with being well informed. We can assist you with any additional advice and information about for example helping your partner to find a job, housing, or schooling. Finally, certain categories of international staff may be eligible for a tax exemption on a part of their salary during the first five years in the Netherlands.

38 hours per week

Droevendaalsesteeg