Bioinformatics, Vol 14, 866-868, Copyright © 1998 by Oxford University Press
WJ Lin and MJ Hwang
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 V
iewer and editor for H elical line M embrane P rotein T opologies) can
automatically generate a schematic 2D topology for a protein with
transmembrane helices. Through an 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. AVAILABILITY: The source code and a user
manual for VHMPT are available for download at http://www.
ibms.sinica.edu.tw/~mjhwang/vhmpt. CONTACT: mjhwang@mail.ibms.sinica.edu.tw
ARTICLES
VHMPT: a graphical viewer and editor for helical membrane protein topologies
Institute of Biomedical Sciences, Academia Sinica, Taipei and Department of Computer and Information Science, National Chiao-Tung University, Hsin Chu, Taiwan.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  L. Skrabanek, F. Campagne, and H. Weinstein Building protein diagrams on the web with the residue-based diagram editor RbDe Nucleic Acids Res., July 1, 2003; 31(13): 3856 - 3858. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Mazur, J. E. Krol, M. Marczak, and A. Skorupska Membrane Topology of PssT, the Transmembrane Protein Component of the Type I Exopolysaccharide Transport System in Rhizobium leguminosarum bv. trifolii Strain TA1 J. Bacteriol., April 15, 2003; 185(8): 2503 - 2511. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H.-L. Lai, T.-H. Lin, Y.-Y. Kao, W.-J. Lin, M.-J. Hwang, and Y. Chern The N Terminus Domain of Type VI Adenylyl Cyclase Mediates Its Inhibition by Protein Kinase C Mol. Pharmacol., September 1, 1999; 56(3): 644 - 650. [Abstract] [Full Text]
|
|