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

Kliment Olechnovič (1, 2) , Sergei Grudinin (1)

1 DAO - Données, Apprentissage et Optimisation
2 Institute of Biotechnology [Vilnius]

Motivation: In 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. Results: We 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 delivers results that correlate highly with the original Voronota method, but does it significantly faster. The new method is 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 Implementation: Voronota-LT software is freely available at https://kliment-olechnovic.github.io/voronota/expansion_lt/.

Mots clés: structural bioinformatics; radical Voronoi tessellation; Laguerre-Voronoi diagram; solvent-accessible surface; atom-atom contact areas

Domaines: Bio-informatique [q-bio.QM]

Kliment Olechnovič, Sergei Grudinin. Voronota-LT: efficient, flexible and solvent-aware tessellation-based analysis of atomic interactions. 2024. ⟨hal-04438320⟩