標題: VHMPT: a graphical viewer and editor for helical membrane protein topologies
作者: Lin, WJ
Hwang, MJ
資訊工程學系
Department of Computer Science
公開日期: 1-一月-1998
摘要: Motivation: Lacking structures resolved at atomic resolution, the great majority of membrane proteins have typically been depicted in a schematic two-dimensional (2D) topology consisting of putative transmembrane domains predicted from hydropathy plots. As more and more sequences of membrane proteins become available from genome projects, there is a need to automate the process of generating the schematic topology while allowing important information, such as the individual amino acid and the extent to which it is conserved in evolution, to be conveniently inspected. We addressed this need by developing a program called VHMPT. Results: VHMPT (a graphical iewer and editor for elical line embrane rotein opologies) can automatically generate a schematic 2D topology for a protein with transmembrane helices. Through art interactive graphical interface, VHMPT allows users to modify the layout of the generated topology, label specific amino acid or amino acid groups, and annotate with arrows and texts. Given a multiple sequence alignment file, VHMPT can also color code a normalized conservation score for each amino acid on the generated topology, allowing ready visual recognition of highly conserved (or variable) topological regions. VHMPT is written in Tcl/Tk and can run on platforms that have installed the Tcl/Tk interpreter.
URI: http://dx.doi.org/10.1093/bioinformatics/14.10.866
http://hdl.handle.net/11536/90
ISSN: 1367-4803
DOI: 10.1093/bioinformatics/14.10.866
期刊: BIOINFORMATICS
Volume: 14
Issue: 10
起始頁: 866
結束頁: 868
顯示於類別:期刊論文


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