Computational Structural Biology

Principal Investigator: Assoc. Prof. Ezgi KARACA

Lab website: https://csb-karacalab.github.io

Karaca Lab studies how biomolecular interfaces form, persist and change. We combine AlphaFold-based sampling, molecular dynamics and integrative modelling to assess the accuracy of predicted assemblies, resolve the interface contacts that determine binding specificity, and extract conformational dynamics from sequence-derived information.

Research Areas

• Benchmarking predictors: How far can structure and affinity predictions be trusted? Through community assessments such as CASP and CAPRI and dedicated benchmarks, we test predictors and build leaner sampling and scoring protocols.
• Interface change: We map how mutations, disease variants and isoforms strengthen, weaken or abolish protein interfaces, and use these maps for functional characterisation and binder design.
• Interface dynamics: Many interface contacts are transient; the persistent ones govern binding. We quantify contact persistence from simulations to find the dynamic networks behind partner choice and function.
• Dynamics in sequence: We extract flexibility signals from AlphaFold distograms and AlphaFold-based sampling to predict interface motions and ensembles directly from sequence.

Software

Our open-source tools (including the PROT-ON web server, DynaPIN, MinnieFold and DistoFlex) are available at https://github.com/CSB-KaracaLab.

Publications

For a complete and up-to-date list, see Google Scholar: https://scholar.google.com/citations?user=5mt6w7MAAAAJ

Projects and Team

Current projects, team members, alumni and supervised theses are listed on the lab website: https://csb-karacalab.github.io

Contact: ezgi.karaca@ibg.edu.tr