A LaTeX package for shaded membrane protein topology plots:
PHD topology predictions are a mighty tool to localize transmembranedomains and the protruding loops. SwissProt databasefiles provide sequence feature informations, such as mutationsites, important domains, or secondary modifications. Makingthese data visible in a sophisticated topology plot is anenormous effort when using a standard drawing software.
TeXtopo is a LaTeX2e macro package that provides two new environments:(a) the 'textopo' environment is used for plotting topology data of membrane proteins derived from PHD predictions,from SwissProt database files or from manually entered datacontaining sequence and transmembrane domain information, and (b) the 'helical wheel' environment draws transmembrane domainsas seen from above or beneath the cell membrane.
Both kinds of plots can be richly decorated with special shadingfor domains of interest, plus labels and legends. TeXtopois fully compatible with TeXshade (v1.3 and up) -- the comprehensivealignment shading package for the TeX community. Thisallows one to apply calculated shading based on sequence conservation and functional aspects of the residue sidechains.
Beitz, E. (2000), TeXtopo: shaded membrane protein topology
plots in LaTeX2e. Bioinformatics 16: 1050-1051. PubMed
- Download the current version of TeXtopo incl. documentation.
- TeXtopo is the engine of a membrane protein topology plotting tool: Protter with a browser-based user interface.