Structuprint: a scalable and extensible tool for two-dimensional representation of protein surfaces
Résumé
Background : The term‘molecular cartography’encompasses a family of computational methods for two-dimensionaltransformation of protein structures and analysis of their physicochemical properties. The underlying algorithmscomprise multiple manual steps, whereas the few existing implementations typically restrict the user to a verylimited set of molecular descriptors. Results : we present Structuprint, a free standalone software that fully automates the rendering of protein surfacemaps, given - at the very least - a directory with a PDB file and an amino acid property. The tool comes with a defaultdatabase of 328 descriptors, which can be extended or substituted by user-provided ones. The core algorithmcomprises the generation of a mould of the protein surface, which is subsequently converted to a sphere andmapped to two dimensions, using the Miller cylindrical projection. Structuprint is partly optimized for multicorecomputers, making the rendering of animations of entire molecular dynamics simulations feasible. Conclusions : Structuprint is an efficient application, implementing a molecular cartography algorithm for proteinsurfaces. 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.
Domaines
Génétique
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