Format

Send to

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

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

Author information

1
Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, UK. d.kontopoulos13@imperial.ac.uk.
2
Bioinformatics & Medical Informatics Team, Biomedical Research Foundation, Academy of Athens, Athens, Greece. dvlachakis@bioacademy.gr.
3
School of Chemical Engineering, National Technical University of Athens, Athens, Greece. gtsiliki@central.ntua.gr.
4
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.

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.

PMID:
26911476
PMCID:
PMC4765231
DOI:
10.1186/s12900-016-0055-7
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for BioMed Central Icon for PubMed Central
Loading ...
Support Center