Structuprint: A Scalable and Extensible Tool for Two-Dimensional Representation of Protein Surfaces

BMC Struct Biol. 2016 Feb 24;16:4. doi: 10.1186/s12900-016-0055-7.

Abstract

Background: The term 'molecular cartography' encompasses a family of computational methods for two-dimensional transformation of protein structures and analysis of their physicochemical properties. The underlying algorithms comprise multiple manual steps, whereas the few existing implementations typically restrict the user to a very limited set of molecular descriptors.

Results: We present Structuprint, a free standalone software that fully automates the rendering of protein surface maps, given - at the very least - a directory with a PDB file and an amino acid property. The tool comes with a default database of 328 descriptors, which can be extended or substituted by user-provided ones. The core algorithm comprises the generation of a mould of the protein surface, which is subsequently converted to a sphere and mapped to two dimensions, using the Miller cylindrical projection. Structuprint is partly optimized for multicore computers, making the rendering of animations of entire molecular dynamics simulations feasible.

Conclusions: Structuprint is an efficient application, implementing a molecular cartography algorithm for protein surfaces. According to the results of a benchmark, its memory requirements and execution time are reasonable, allowing it to run even on low-end personal computers. We believe that it will be of use - primarily but not exclusively - to structural biologists and computational biochemists.

MeSH terms

  • Algorithms
  • Escherichia coli Proteins / chemistry
  • Protein Conformation*
  • Software*
  • Surface Properties
  • User-Computer Interface

Substances

  • Escherichia coli Proteins