Researcher in Protein structure evolution

Updated: 3 months ago

SciLifeLab is a national center for molecular biosciences with a focus on health and environmental research. The center combines frontline technical expertise with advanced knowledge of translational medicine and molecular bioscience. SciLifeLab is a national resource hosted by Karolinska Institutet, KTH Royal Institute of Technology, Stockholm University and Uppsala University. The center also collaborates with several other universities.

The employment will be placed at the Department of biochemistry and biophysics, at Stockholm university.

Project description
Protein structure is essential for understanding their function and developing drugs targeting proteins. Recently, a deep learning method that can predict the structure of most proteins was made freely available, and a database with predicted structure was released. However, proteins do not act alone – they work together with other proteins. Therefore, the next major challenge is using these methods for predicting protein-protein interactions. Our initial studies have shown that it is possible to predict accurate structures of a large part of dimeric proteins using either a modified version of AlphaFold2 or AlphaFold-multimer. However, many proteins cannot be built accurately, nor can we always distinguish interacting from non-interacting protein pairs, and building larger complexes accurately is still an unsolved problem. In this project, we are recruiting two postdocs to leverage recent advances in machine learning to build better deep-learning models for predicting protein-protein interactions and to apply these methods to biologically relevant problems.

The Elofsson group is located at the Science for Life Laboratory. Elofsson has worked on protein structure predictions for more than two decades. He has worked on various techniques using machine learning and other computational techniques. His most important contributions to this work are the methods he has developed to identify the quality of protein models, Pcons, and various versions of ProQ. The group comprises 5 Ph.D. students, 2 PostDocs, and one senior researcher.

Main responsibilities
The project consists of three parts (1)  Identification of all human proteoforms, (2)  identification of all protein-protein interactions, and  (3) modeling of all protein complexes. A critical part of this position is coordinating the work within these subprojects.

Qualification requirements
Researchers are appointed primarily for purposes of research and must hold a Swedish doctoral degree or an equivalent degree from another country.

Assessment criteria
In the appointment process, special attention will be given to research skills. Applicants with a Ph.D. in bioinformatics are eligible. Suitable backgrounds are a Ph.D. in computer science, bioinformatics, or a related field. Good programming and management skills, knowledge of proteins, and deep learning are advantages.

Terms of employment
The position involves full-time employment for a maximum of 11 months. Start date 2024-01-01 or as per agreement.

Stockholm University strives to be a workplace free from discrimination and with equal opportunities for all.

Contact
Further information about the position can be obtained from Professor Arne Elofsson, telephone: +46 76 95 10 45, [email protected] .



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