About

Ezgi Karaca is a computational structural biologist who aims to understand the underlying mechanics of biomolecular interactions. Her journey began at Utrecht University, where she completed her Ph.D. in 2013 under the supervision of Prof. Alexandre Bonvin. During this time, she focused on advancing HADDOCK, one of the flagship BioExcel software codes. She then moved to EMBL Heidelberg for her postdoctoral research (2013–2016), working with Prof. Teresa Carlomagno and Prof. Orsolya Barabas. There, she developed M3, a HADDOCK-centered modeling tool for large-scale complexes using sparse experimental data (https://www.nature.com/articles/nmeth.4392). In 2017, she established the Computational Structural Biology Lab at Izmir Biomedicine and Genome Center and joined Dokuz Eylul University (https://ibg.edu.tr/ezgi-karaca-en). Since then, her lab has been aiming to be a hub for developing both classical and AI-driven approaches to model biomolecular interactions.

Research interests

Ezgi’s research centers on the structural prediction of biomolecular complexes and the dynamics of protein interfaces. A significant milestone for her lab was the launch of PROT-ON, a structure-based web server for designing interfacial mutations (http://proton.tools.ibg.edu.tr:8001/). It has seen incredible adoption, currently facilitating roughly 50,000 runs per year for researchers worldwide. She is also honored to have received an EMBO Installation Grant (2020) and to have served as the first assessor from Türkiye for the assembly prediction rounds in CASP14 and CASP15, contributing to the community’s evaluation of the state-of-the-art in protein assembly.

Working with BioExcel

BioExcel has been a very important resource throughout Ezgi’s career. In the early years of her lab, she was not an expert in Molecular Dynamics (MD). During that time, she used several tools and resources from BioExcel to find the best MD protocols for her research. This support helped her establish reliable workflows in the lab.

BioExcel is also a key part of her group’s education. Three of her students attended the BioExcel Summer School, where they learned a lot and brought that knowledge back to the team. Additionally, she personally follows the BioExcel webinars closely to keep herself and her lab updated on the latest developments in the field. As she moves toward developing new AI-driven models to predict dynamic protein interfaces, she expects BioExcel’s expertise in high-performance computing and workflows will continue to be of crucial support for them.

Learn more about the BioExcel Ambassador Program