Date: 31 March 2026
Time: 15:00 CET
Abstract
Static structural models often fail to capture the dynamic mechanisms of protein interactions. To address this, we introduce DynaPIN, an open-source pipeline for extracting dynamic interface fingerprints from molecular simulations. DynaPIN unifies quality control metrics, interface prediction accuracy assessment, and atomistic interaction analysis into a single automated workflow, accessible at https://github.com/CSB-KaracaLab/DynaPIN. A key feature is our interface-specific analysis centered on a Dynamic Interface definition, which classifies residues based on the persistence of their interaction status over the simulation. We applied DynaPIN to representative rigid, medium, and difficult targets from the DynaBench dataset, an MD simulation resource for Docking Benchmark 5.5. Our results show that interface flexibility diverges from static accuracy classifications established in Docking Benchmark 5.5, as explored before. All in all, by providing standardized, frame-resolved outputs, DynaPIN’s aim is to facilitate mechanistic studies and generate standardized unbiased data for future dynamics-aware artificial intelligence models.
Presenters
Ezgi Karaca
Ezgi Karaca is a computational structural biologist specializing in structural modeling and biomolecular dynamics. She completed her Ph.D. (2013) at Utrecht University under the supervision of Prof. Alexandre Bonvin, where she advanced HADDOCK. She then conducted her postdoctoral research at EMBL Heidelberg (2013–2016) with Prof. Teresa Carlomagno and Prof. Orsolya Barabas, developing M3, a protein complex modeling tool capable of handling 20 molecules using sparse experimental data. In 2017, Dr. Karaca established the Computational Structural Biology Lab at Izmir Biomedicine and Genome Center and joined Dokuz Eylul University. Her lab develops classical and AI-driven approaches to model biomolecular interactions and their dynamics. She received an EMBO Installation Grant (2020). Dr. Karaca was also the first assessor from Türkiye in CASP14 and CASP15 for the assembly prediction rounds. Her lab’s first online tool, PROT-ON, a structure-based web server for designing interfacial mutations, gained significant attention from the scientific community, with 50,000 uses per year worldwide.
Bluesky: @ezgikaraca.bsky.social
LinkedIn: @ezgi-karaca-ibg
Ayşe Berçin Barlas
Ayşe Berçin Barlas is a computational structural biologist specialized in molecular dynamics simulations and biomolecular interface analysis. She completed her Ph.D. at the Izmir Biomedicine and Genome Center (IBG) and Dokuz Eylül University under the supervision of Dr. Ezgi Karaca, where she investigated how biomolecular complexes encode functional specificity through dynamics. During her doctoral research, she developed a Comparative Dynamics Analysis (CDA) framework to dissect molecular basis of sequence-specific DNA recognition by methyltransferases. As a postdoctoral researcher at IBG, Dr. Barlas is currently working on the development of DynaPIN, a Python-based package for time-resolved characterization of protein-protein interfaces. She is also one of the contributors of DynaBench, a large-scale molecular dynamics dataset designed to capture interface dynamics beyond static reference structures.
