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Shape tracing: An extension of sphere tracing for 3D non-convex collision in protein docking

Leach, Adam and Rudden, Lucas S.P. and Bond-Taylor, Sam and Brigham, John C. and Degiacomi, Matteo T. and Willcocks, Chris G. (2020) 'Shape tracing: An extension of sphere tracing for 3D non-convex collision in protein docking.', in 2020 IEEE 20th International Conference on Bioinformatics and Bioengineering (BIBE). , pp. 49-52.

Abstract

This paper presents an algorithm, similar to implicit sphere tracing, that ray marches 3D non-convex shapes for efficient collision detection. Instead of finding points on the surface where individual rays strike, an entire shape is marched in unison by a lower bound of the boundary distance, calculated at the closest point between the two surfaces. Advancing one shape towards the other by this new bound allows us to identify a contact in few steps. This method supports arbitrary nonconvex shapes, and can be run in parallel. We apply this to protein-protein docking and show that we can identify around 80 docking poses per second featuring contact but no overlap, irrespective of proteins’ specific geometry. This paves the way to future fast docking algorithms, building upon implicit surface representations to quickly find a well-distributed subset of close candidate solutions for further investigation.

Item Type:Book chapter
Full text:(AM) Accepted Manuscript
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Status:Peer-reviewed
Publisher Web site:https://doi.org/10.1109/BIBE50027.2020.00016
Publisher statement:© 2020 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.
Date accepted:No date available
Date deposited:07 April 2021
Date of first online publication:26 October 2020
Date first made open access:07 April 2021

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