Structuprint: a scalable and extensible tool for two-dimensional representation of protein surfaces

Area of Science:

• Structural Biology
• Computational Biochemistry
• Bioinformatics

Background:

• Molecular cartography involves computational methods for 2D transformation of protein structures and physicochemical property analysis.
• Existing algorithms often require manual steps and offer limited molecular descriptors.

Purpose of the Study:

• To introduce Structuprint, a novel software for automating molecular cartography.
• To provide a user-friendly tool for generating protein surface maps with extensive descriptor options.

Main Methods:

• Structuprint automates the rendering of protein surface maps using a PDB file and amino acid properties.
• The core algorithm generates a protein surface mould, converts it to a sphere, and maps it to 2D using Miller cylindrical projection.
• The software is optimized for multicore processors, enabling molecular dynamics simulation animations.

Main Results:

• Structuprint is a free, standalone software that fully automates protein surface map generation.
• It includes a default database of 328 descriptors, expandable by users.
• Animations of molecular dynamics simulations are feasible due to multicore optimization.

Conclusions:

• Structuprint is an efficient application for molecular cartography of protein surfaces.
• Its reasonable memory and execution times allow use on low-end personal computers.
• The software is expected to benefit structural biologists and computational biochemists.