Summary

Given an input molecular structure, the VoroContacts server runs the Voronota software to perform the following actions:

• Compute the Voronoi tessellation of atomic balls.
• Calculate interatomic contact areas based on the tessellation.
• Query contact information using user-provided parameters.

References

This web server is presented in

• Kliment Olechnovic and Ceslovas Venclovas. VoroContacts: a tool for the analysis of interatomic contacts in macromolecular structures. Bioinformatics (2021) 10.1093/bioinformatics/btab448. PubMed ID 34132767.

Our method for computing the Voronoi tessellation was presented in

• Kliment Olechnovic and Ceslovas Venclovas. Voronota: A fast and reliable tool for computing the vertices of the Voronoi diagram of atomic balls. J Comput Chem (2014) 10.1002/jcc.23538. PubMed ID 24523197.

Our current methodology for the computation of interatomic contacts was first presented in

• Kliment Olechnovic and Ceslovas Venclovas. VoroMQA: Assessment of protein structure quality using interatomic contact areas. Proteins (2017) 10.1002/prot.25278. PubMed ID 28263393.

The contact querying capabilities were first presented in

• Kliment Olechnovic and Ceslovas Venclovas. Contact Area-Based Structural Analysis of Proteins and Their Complexes Using CAD-Score. Zoltan Gaspari (eds) Structural Bioinformatics: Methods and Protocols, Methods in Molecular Biology, vol. 2112. Springer (2020).

Below are some graphical illustrations of our methodology.

Voronoi tessellation of balls

Deriving interatomic contacts from the Voronoi tessellation of balls

Constraining interatomic contacts inside the solvent-accessible surface

Defining the interface between groups of atoms using the tessellation derived contacts

Example of an interface: interface between two protein chains