Bilkent University
Department of Computer Engineering

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CS 590/690 SEMINAR

 

RPDockDiff: A Diffusion-Based Framework for RNA–Protein Rigid Docking and Structure Refinement

 

Helyasadat Hashemi Aghdam
Master Student
(Supervisor:Assoc.Prof.Ercüment Çiçek)

Computer Engineering Department
Bilkent University

Abstract: RNA–protein interactions are important for many biological processes, such as gene regulation and cellular function. However, predicting how RNA and proteins bind to each other is still a challenging problem, especially in rigid docking. In this project, we present a diffusion-based approach for RNA–protein rigid docking that learns translation and rotation between molecules. Our model uses a diffusion process to gradually improve the position and orientation of RNA and protein structures. Starting from an initial complex, the model refines the binding pose step by step by applying learned transformations. In addition to docking, our method can also be used to refine RNA–protein complex structures predicted by tools such as AlphaFold3. We also address an important data limitation in this field by creating a large RNA–protein dataset. Since most structures in the PDB are ribosomal (around 95%), many models become biased toward this type of complex. To avoid this problem, we construct a more balanced dataset that includes both ribosomal and non-ribosomal complexes, which helps our model generalize better and reduces bias. Overall, this work shows that diffusion-based methods can be effective for RNA–protein docking and structure refinement.

 

DATE: March 30, Monday @ 15:30 Place: EA 502