Abstract
BackgroundThe 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.ResultsWe 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.ConclusionsStructuprint 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12900-016-0055-7) contains supplementary material, which is available to authorized users.
Highlights
The term ‘molecular cartography’ encompasses a family of computational methods for two-dimensional transformation of protein structures and analysis of their physicochemical properties
A few applications that implement molecular cartography algorithms are available (SURF’S UP! [8], PST [9], Udock [10]), but the range of supported physicochemical descriptors for visualization is typically limited to charge and hydrophobicity
To transfer the dummy atoms onto the surface of a sphere, each vector v'i is scaled to a length equal to the radius: Map smoothing The previous step resulted in a map of the protein surface with data points coloured by a property of choice
Summary
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
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