Efficient GPU Computation of Large Protein Solvent-Excluded Surface

The Solvent-Excluded Surface (SES) is an essential representation of molecules which is massively used in molecular modeling and drug discovery since it represents the interacting surface between molecules. Based on its properties, it supports the visualization of both large scale shapes and details...

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Bibliographic Details
Published in:IEEE transactions on visualization and computer graphics Vol. 31; no. 4; pp. 2101 - 2113
Main Authors: PlateauHolleville, Cyprien, Maria, Maxime, Merillou, Stephane, Montes, Matthieu
Format: Journal Article
Language:English
Published: United States IEEE 01.04.2025
Institute of Electrical and Electronics Engineers
Subjects:
Biochemistry, Molecular Biology
Bioinformatics
Computer Science
Distributed, Parallel, and Cluster Computing
Geometry
Graphics
Graphics processing units
Life Sciences
massively parallel algorithms
Memory management
Proteins
Rendering (computer graphics)
Scientific visualization
Structural Biology
Surface treatment
Synthetic aperture sonar
Massively parallel algorithms
Scientific visualization
ISSN:1077-2626, 1941-0506, 1941-0506
Online Access:Get full text
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Summary:The Solvent-Excluded Surface (SES) is an essential representation of molecules which is massively used in molecular modeling and drug discovery since it represents the interacting surface between molecules. Based on its properties, it supports the visualization of both large scale shapes and details of molecules. While several methods targeted its computation, the ability to process large molecular structures to address the introduction of big complex analysis while leveraging the massively parallel architecture of GPUs has remained a challenge. This is mostly caused by the need for consequent memory allocation or by the complexity of the parallelization of its processing. In this paper, we leverage the last theoretical advances made for the depiction of the SES to provide fast analytical computation with low impact on memory. We show that our method is able to compute the complete surface while handling large molecular complexes with competitive computation time costs compared to previous works.
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ISSN:1077-2626
1941-0506
1941-0506
DOI:10.1109/TVCG.2024.3380100