Bioinformatics Vol. 17 no. 9 2001
Pages 849-850
© 2001 Oxford University Press
Applications Note |
The HMMTOP transmembrane topology prediction server
1 Institute of Enzymology, BRC, Hungarian
Academy of Sciences, H-1518 Budapest, PO Box 7, Hungary
2 Department of Biological Physics,
Eötvös
Loránd University, H-1117 Budapest,
Pázmány
P.
sétány
1, Hungary
Received on March 7, 2001
; revised on April 27, 2001
; accepted on May 28, 2001
Summary: The HMMTOP transmembrane topology prediction server predicts both the localization of helical transmembrane segments and the topology of transmembrane proteins. Recently, several improvements have been introduced to the original method. Now, the user is allowed to submit additional information about segment localization to enhance the prediction power. This option improves the prediction accuracy as well as helps the interpretation of experimental results, i.e. in epitope insertion experiments.
Availability: HMMTOP 2.0 is freely available to non-commercial users at http://www.enzim.hu/hmmtop. Source code is also available upon request to academic users.
Contact: tusi{at}enzim.hu
* To whom correspondence should be addressed.
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A. K. Singh, R. Haldar, D. Mandal, and M. Kundu Analysis of the Topology of Vibrio cholerae NorM and Identification of Amino Acid Residues Involved in Norfloxacin Resistance Antimicrob. Agents Chemother., November 1, 2006; 50(11): 3717 - 3723. [Abstract] [Full Text] [PDF]
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 T. Beuming, L. Shi, J. A. Javitch, and H. Weinstein A Comprehensive Structure-Based Alignment of Prokaryotic and Eukaryotic Neurotransmitter/Na+ Symporters (NSS) Aids in the Use of the LeuT Structure to Probe NSS Structure and Function Mol. Pharmacol., November 1, 2006; 70(5): 1630 - 1642. [Abstract] [Full Text] [PDF]
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R. C. Elble, V. Walia, H.-c. Cheng, C. J. Connon, L. Mundhenk, A. D. Gruber, and B. U. Pauli The Putative Chloride Channel hCLCA2 Has a Single C-terminal Transmembrane Segment J. Biol. Chem., October 6, 2006; 281(40): 29448 - 29454. [Abstract] [Full Text] [PDF]
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L. Mundhenk, M. Alfalah, R. C. Elble, B. U. Pauli, H. Y. Naim, and A. D. Gruber Both Cleavage Products of the mCLCA3 Protein Are Secreted Soluble Proteins J. Biol. Chem., October 6, 2006; 281(40): 30072 - 30080. [Abstract] [Full Text] [PDF]
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K. Hiller, A. Grote, M. Maneck, R. Munch, and D. Jahn JVirGel 2.0: computational prediction of proteomes separated via two-dimensional gel electrophoresis under consideration of membrane and secreted proteins Bioinformatics, October 1, 2006; 22(19): 2441 - 2443. [Abstract] [Full Text] [PDF]
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 D. P. Terwilliger, K. M. Buckley, D. Mehta, P. G. Moorjani, and L.C. Smith Unexpected diversity displayed in cDNAs expressed by the immune cells of the purple sea urchin, Strongylocentrotus purpuratus Physiol Genomics, September 14, 2006; 26(2): 134 - 144. [Abstract] [Full Text] [PDF]
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M. Quick, H. Yano, N. R. Goldberg, L. Duan, T. Beuming, L. Shi, H. Weinstein, and J. A. Javitch State-dependent Conformations of the Translocation Pathway in the Tyrosine Transporter Tyt1, a Novel Neurotransmitter:Sodium Symporter from Fusobacterium nucleatum J. Biol. Chem., September 8, 2006; 281(36): 26444 - 26454. [Abstract] [Full Text] [PDF]
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M. Fujiki, S. Kawakami, R. W. Kim, and R. N. Beachy Domains of tobacco mosaic virus movement protein essential for its membrane association J. Gen. Virol., September 1, 2006; 87(9): 2699 - 2707. [Abstract] [Full Text] [PDF]
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H. Kim, K. Melen, M. Osterberg, and G. von Heijne A global topology map of the Saccharomyces cerevisiae membrane proteome PNAS, July 25, 2006; 103(30): 11142 - 11147. [Abstract] [Full Text] [PDF]
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H. Nakanishi, H. Shindou, D. Hishikawa, T. Harayama, R. Ogasawara, A. Suwabe, R. Taguchi, and T. Shimizu Cloning and Characterization of Mouse Lung-type Acyl-CoA:Lysophosphatidylcholine Acyltransferase 1 (LPCAT1): EXPRESSION IN ALVEOLAR TYPE II CELLS AND POSSIBLE INVOLVEMENT IN SURFACTANT PRODUCTION J. Biol. Chem., July 21, 2006; 281(29): 20140 - 20147. [Abstract] [Full Text] [PDF]
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F. Mueller, D. J. Muller, and D. Labudde Analysis assistant for single-molecule force spectroscopy data on membrane proteins--MPTV Bioinformatics, July 15, 2006; 22(14): 1796 - 1799. [Abstract] [Full Text] [PDF]
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S.-H. Cho and J. Beckwith Mutations of the Membrane-Bound Disulfide Reductase DsbD That Block Electron Transfer Steps from Cytoplasm to Periplasm in Escherichia coli. J. Bacteriol., July 1, 2006; 188(14): 5066 - 5076. [Abstract] [Full Text] [PDF]
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S. Lee, B. Lee, I. Jang, S. Kim, and J. Bhak Localizome: a server for identifying transmembrane topologies and TM helices of eukaryotic proteins utilizing domain information. Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W99 - W103. [Abstract] [Full Text] [PDF]
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 G. G. J. M. Kuiper, W. Klootwijk, G. Morvan Dubois, O. Destree, V. M. Darras, S. Van der Geyten, B. Demeneix, and T. J. Visser Characterization of Recombinant Xenopus laevis Type I Iodothyronine Deiodinase: Substitution of a Proline Residue in the Catalytic Center by Serine (Pro132Ser) Restores Sensitivity to 6-Propyl-2-Thiouracil Endocrinology, July 1, 2006; 147(7): 3519 - 3529. [Abstract] [Full Text] [PDF]
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B. T. F. Alako, D. Rainey, H. Nijveen, and J. A. M. Leunissen TreeDomViewer: a tool for the visualization of phylogeny and protein domain structure. Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W104 - W109. [Abstract] [Full Text] [PDF]
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M. Novatchkova, G. Schneider, R. Fritz, F. Eisenhaber, and A. Schleiffer DOUTfinder--identification of distant domain outliers using subsignificant sequence similarity. Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W214 - W218. [Abstract] [Full Text] [PDF]
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 M.-J. Han and S. Y. Lee The Escherichia coli Proteome: Past, Present, and Future Prospects Microbiol. Mol. Biol. Rev., June 1, 2006; 70(2): 362 - 439. [Abstract] [Full Text] [PDF]
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P. Saini, N. A. Gaur, and R. Prasad Chimeras of the ABC drug transporter Cdr1p reveal functional indispensability of transmembrane domains and nucleotide-binding domains, but transmembrane segment 12 is replaceable with the corresponding homologous region of the non-drug transporter Cdr3p. Microbiology, May 1, 2006; 152(Pt 5): 1559 - 1573. [Abstract] [Full Text] [PDF]
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