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bioRxiv · 10.1101/2024.02.05.577169

Voronota-LT: efficient, flexible and solvent-aware tessellation-based analysis of atomic interactions

Olechnovic, K.·Grudinin, S.
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Abstract

MotivationIn the fields of structural biology and bioinformatics, understanding molecular interactions is paramount. However, existing advanced geometric methods for describing interatomic contacts considering full structural context have typically demanded substantial computational resources, hindering their practical application. Given the ever-growing volume of structural data, there is an urgent need for more efficient tools for interaction analysis. ResultsWe present Voronota-LT, a new efficient method tailored for computing Voronoi tessellation-based atom-atom contacts within the solvent-accessible surface of molecular structures. Voronota-LT constructs every interatomic contact surface directly, without pre-computing the global Voronoi diagram or Delaunay triangulation. This approach results in a method that is not only fast, but also parallelizable and capable of selectively targeting specific interface areas within molecular complexes. While offering high execution speed, Voronota-LT provides a comprehensive description of every interatomic interaction, taking full account of the relevant structural context. Availability and ImplementationVoronota-LT software is freely available as both a standalone application and a C++ header-only library at https://kliment-olechnovic.github.io/voronota/expansion_lt/.

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Olechnovic, K., Grudinin, S.. 2024-02-05. Voronota-LT: efficient, flexible and solvent-aware tessellation-based analysis of atomic interactions. https://doi.org/10.1101/2024.02.05.577169

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