title: Structuprint: a scalable and extensible tool for two-dimensional representation of protein surfaces.
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.
authors.affiliation: Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, UK. d.kontopoulos13@imperial.ac.uk.
authors.forename: Dimitrios Georgios
authors.initials: DG
authors.lastname: Kontopoulos
authors.affiliation: Bioinformatics & Medical Informatics Team, Biomedical Research Foundation, Academy of Athens, Athens, Greece. dvlachakis@bioacademy.gr.
authors.forename: Dimitrios
authors.initials: D
authors.lastname: Vlachakis
authors.affiliation: School of Chemical Engineering, National Technical University of Athens, Athens, Greece. gtsiliki@central.ntua.gr.
authors.forename: Georgia
authors.initials: G
authors.lastname: Tsiliki
authors.affiliation: IMGT®, The International ImMunoGeneTics Information System®, Université de Montpellier, Laboratoire d'ImmunoGénétique Moléculaire LIGM, UPR CNRS 1142, Institut de Génétique Humaine, Montpellier, France. sofia.kossida@igh.cnrs.fr.
authors.forename: Sofia
authors.initials: S
authors.lastname: Kossida
mesh_terms: D000465:Algorithms; D029968:Escherichia coli Proteins / Q000737:chemistry; D011487:Protein Conformation; D012984:Software; D013499:Surface Properties; D014584:User-Computer Interface
chemical_list: D029968:Escherichia coli Proteins