Skip Navigation


Bioinformatics Advance Access originally published online on June 4, 2004
Bioinformatics 2004 20(17):2964-2972; doi:10.1093/bioinformatics/bth340
This Article
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow FREE Full Text (Screen PDF)
Right arrow All Versions of this Article:
20/17/2964    most recent
bth340v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (28)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Tusnády, G. E.
Right arrow Articles by Simon, I.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Tusnády, G. E.
Right arrow Articles by Simon, I.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Bioinformatics vol. 20 issue 17 © Oxford University Press 2004; all rights reserved.

Transmembrane proteins in the Protein Data Bank: identification and classification

Gábor E. Tusnády , Zsuzsanna Dosztányi and István Simon *

Institute of Enzymology, BRC, Hungarian Academy of Sciences, Budapest, Hungary

Received on January 23, 2004; revised on April 9, 2004; accepted on May 25, 2004
Advance Access Publication June 4, 2004

Motivation: Integral membrane proteins play important roles in living cells. Although these proteins are estimated to constitute 25% of proteins at a genomic scale, the Protein Data Bank (PDB) contains only a few hundred membrane proteins due to the difficulties with experimental techniques. The presence of transmembrane proteins in the structure data bank, however, is quite invisible, as the annotation of these entries is rather poor. Even if a protein is identified as a transmembrane one, the possible location of the lipid bilayer is not indicated in the PDB because these proteins are crystallized without their natural lipid bilayer, and currently no method is publicly available to detect the possible membrane plane using the atomic coordinates of membrane proteins.

Results: Here, we present a new geometrical approach to distinguish between transmembrane and globular proteins using structural information only and to locate the most likely position of the lipid bilayer. An automated algorithm (TMDET) is given to determine the membrane planes relative to the position of atomic coordinates, together with a discrimination function which is able to separate transmembrane and globular proteins even in cases of low resolution or incomplete structures such as fragments or parts of large multi chain complexes. This method can be used for the proper annotation of protein structures containing transmembrane segments and paves the way to an up-to-date database containing the structure of all known transmembrane proteins and fragments (PDB_TM) which can be automatically updated. The algorithm is equally important for the purpose of constructing databases purely of globular proteins.

Availability: The PDB_TM database is available for academic users on http://www.enzim.hu/PDB_TM.

Supplementary information: Data files used in this article can be found under the PDB_TM homepage (http://www.enzim.hu/PDB_TM/index.php?method=docs).

Contact: tusi{at}enzim.hu, zsuzsa{at}enzim.hu, simon{at}enzim.hu

* To whom correspondence should be addressed.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Nucleic Acids ResHome page
A. Marsico, K. Scheubert, A. Tuukkanen, A. Henschel, C. Winter, R. Winnenburg, and M. Schroeder
MeMotif: a database of linear motifs in {alpha}-helical transmembrane proteins
Nucleic Acids Res., November 12, 2009; (2009) gkp1042v1.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
Y. Park and V. Helms
Prediction of the translocon-mediated membrane insertion free energies of protein sequences
Bioinformatics, May 15, 2008; 24(10): 1271 - 1277.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
G. E. Tusnady, L. Kalmar, and I. Simon
TOPDB: topology data bank of transmembrane proteins
Nucleic Acids Res., January 11, 2008; 36(suppl_1): D234 - D239.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
M. A. Lomize, A. L. Lomize, I. D. Pogozheva, and H. I. Mosberg
OPM: Orientations of Proteins in Membranes database
Bioinformatics, March 1, 2006; 22(5): 623 - 625.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
B. Cao, A. Porollo, R. Adamczak, M. Jarrell, and J. Meller
Enhanced recognition of protein transmembrane domains with prediction-based structural profiles
Bioinformatics, February 1, 2006; 22(3): 303 - 309.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
A. G. Garrow, A. Agnew, and D. R. Westhead
TMB-Hunt: a web server to screen sequence sets for transmembrane {beta}-barrel proteins
Nucleic Acids Res., July 1, 2005; 33(suppl_2): W188 - W192.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
G. E. Tusnady, Z. Dosztanyi, and I. Simon
TMDET: web server for detecting transmembrane regions of proteins by using their 3D coordinates
Bioinformatics, April 1, 2005; 21(7): 1276 - 1277.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.