GPU-accelerated Cartoon Representation for Interactive Flexible Docking

Holdsworth, Katerina, Iakovou, Georgios, Hayward, Steven and Laycock, Stephen (2025) GPU-accelerated Cartoon Representation for Interactive Flexible Docking. In: Computer Graphics and Visual Computing (CGVC). UNSPECIFIED.

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Abstract

Molecular docking involves simulating the binding of two biomolecules, a receptor and ligand, and is widely used for structurebased drug design. There are two main types of docking tools: automated and interactive. While automated tools are useful for reducing the search space of ligands and identifying potential binding sites, interactive tools allow the user to guide the docking process and observe what happens during docking. High computation speeds are required for interactive docking to handle both protein deformation and user interaction in real time. The cartoon representation, not to be confused with cartoon style rendering, is a protein representation that shows an abstracted view and is frequently used by structural biologists to not only identify a protein, but also to identify key regions within a protein of interest. There are examples of GPU-accelerated methods to construct the cartoon representation in real time. However, none of these methods achieve real-time assignment of secondary structure and construction of the cartoon representation for a flexible molecule. This paper presents our method to achieve this, integrated into an interactive docking tool with receptor flexibility. The methods outlined in this paper produced some promising results, with proteins of up to 3,300 amino acid residues being constructed and rendered at 70 fps.

Item Type:	Book Section
Faculty \ School:	Faculty of Science > School of Computing Sciences
UEA Research Groups:	Faculty of Science > Research Groups > Visual Computing and Signal Processing Faculty of Science > Research Groups > Computational Biology Faculty of Science > Research Groups > Health Technologies
Depositing User:	LivePure Connector
Date Deposited:	18 Sep 2025 09:32
Last Modified:	22 Sep 2025 00:07
URI:	https://ueaeprints.uea.ac.uk/id/eprint/100436
DOI:	10.2312/cgvc.20251222

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