Structure-based detection of critical mutations in redesigning protein-protein interfaces

Scientific Context of the Project

Uncovering the principles of protein-protein interactions is essential for dissecting their biomolecular function. Computational methods developed based on this idea have recently been able to redesign the available biomolecular interactions. It has been shown that a handful of such methodologies could gain some proteins a new function. Considering the time course of the evolution, being able to re-model protein interactions in the computer environment is an unprecedented development. Therefore, day by day, the protein interaction re-design field has been gaining popularity. Though, the fact that the existing methods;

(i) have a complicated algorithm,

(ii) are not flexible enough to adapt themselves toward different binding types,

(iii) are unable to make predictions of opposite characteristics, such as mutations that both enhance or abolish binding,

(iv) do not have a scoring function that can eliminate noisy solutions via a statistics-based function,

(v) do require big computational resources, which are unreachable for many institutions,

creates an avenue for methodological improvement.

Innovative Aspects of the Project

Taking the above-described problems into account, we will design the PROT-ON method, which aims at determining critical mutations that can strengthen or weaken protein-protein interactions based on the available protein complexes. PROT-ON targets to realize this objective in a reliable, flexible, and accessible manner.

Research Environment and Infrastructure

IBG (Izmir Biomedicine and Genome Center) is the first independent and international life sciences research institution of Turkey. It is established with the aim of being a prominent health sciences hub in the MENA and South European regions. It has 28 independent basic and translational research groups working in diverse areas, such as genomics, epigenetics, bioinformatics, cancer biology, and bioengineering.

Karaca Lab situation in IBG offers spacious office space and the necessary high performance computing facility required to carry out the proposed project. Karaca Lab also works in close collaboration with the bioinformatics and several experimental departments of IBG (

Project Acronym


Main Supervisor

Asst. Prof. Ezgi Karaca (IBG)


Assoc. Prof. Gökhan Karakulah (IBG)

Asst. Prof. Işıl Öz (IZTECH)

Recruiting Institution

Dokuz Eylül University, Izmir International Biomedicine and Genome Institute, Dokuz Eylul University Health Campus, Balcova/İzmir

PhD Awarding Institution

Dokuz Eylül University, Izmir International Biomedicine and Genome Institute

PhD Title

PhD in Biomedicine and Health Technologies

International Academic Secondment

Polytechnic University of Catalonia, Barcelona, Spain

Intersectoral Mobility

Solaris Genomic Health (TR) and Istanbul Health Industry Cluster (ISEK)