Original scientific paper

Precise Annotation of Transmembrane Segments with Garlic – a Free Molecular Visualization Program

Damir Zucić ; School of Medicine, University of Osijek, J. Huttlera 4, 31000 Osijek, Croatia
Davor Juretić ; Physics Department, Faculty of Natural Sciences, Mathematics and Education, University of Split, N. Tesle 12, 21000 Split, Croatia

Abstract

Comparison of transmembrane secondary structure prediction programs requires precise annotations of transmembrane segments of known proteins. Annotations that may be found in different databases differ significantly due to the lack of a standard method for annotation of transmembrane segments. Simple methods for the placement of a bilayer membrane with respect to the known 3D structure of membrane protein were developed to improve precise determination of the transmembrane portion of the protein. The methods were implemented in the freely available, open-source molecular visualization program called Garlic. The program, complete with the source code and extensive documentation, may be found at the site: http://garlic.mefos.hr/garlic.

Keywords

membrane proteins; transmembrane part; molecular visualization; membrane model; hydrophobicity

Hrčak ID:

102733

URI

https://hrcak.srce.hr/102733

Publication date:

31.5.2004.

Visits: 1.198 *