The HMMTOP transmembrane topology prediction server

By Gábor E. Tusnády, István Simon. Bioinform., 2001

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Subfields: Law, Political Science and International Relations

View Paper: https://www.semanticscholar.org/paper/55871e3ea3a02767f00a3c4a5a2a55554f0171ba

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Citations in the corpus

TCDB: the Transporter Classification Database for membrane transport protein analyses and information (2005, methodology): “Several tools to analyze transporters are provided such as TMS prediction using HMMTOP 2.0 (20), hydropathy analysis using the Kyte and Doolittle hydro-pathy scale (21), hydrophobic moment (amphipathicity) analysis (22) using the H moment program from EMBOSS (23) and helical wheel plots using the…”
Transmembrane protein topology prediction using support vector machines (2009, methodology): “Methods include HMM-TM [11], HMMTOP [12] and TMHMMfix [13].”
P2CS: a two-component system resource for prokaryotic signal transduction research (2009, methodology): “Finally, the cellular localization of each TCS protein was determined by the presence or absence of transmembrane (TM) segments, using the HMMTOP predictor [14].”
CCTOP: a Consensus Constrained TOPology prediction web server (2015, methodology): “The prediction results of these meth-ods are used as constraints in the same hidden Markov model that was used by HMMTOP but with different weights.”
TOPCONS: consensus prediction of membrane protein topology (2009, methodology): “Using a dataset of 163 sequences with known topology, the performance of TOPCONS was benchmarked against eight other topology prediction algorithms (Table 1). ConPredII (7) is an earlier consensus transmembrane topology prediction approach, and the other methods [OCTOPUS (9), MEMSAT3 (13), SCAMPI (1”
Atypical Membrane Topology and Heteromeric Function of Drosophila Odorant Receptors In Vivo (2006, methodology): “Membrane topology predictions of OR sequences were examined using HMMTOP version 2.0 [ 48 ], TMHMM Server version 2.0 [49], and transmembrane prediction [50].”
PSORT-B: improving protein subcellular localization prediction for Gram-negative bacteria (2003, methodology): “PSORT-B utilizes the Hidden Markov Modelbased method HMMTOP (15, 16 ) to identify potential transmembrane alpha helices, assigning a localization of inner membrane if three or more helices are found.”
The cellulose synthase superfamily. (2000, positive): “Transmembrane domains predicted with HmmTop v2.0 ( Tusnady and Simon 2001 ).”
VacSol: a high throughput in silico pipeline to predict potential therapeutic targets in prokaryotic pathogens using subtractive reverse vaccinology (2017, methodology): “HMMTOP version 2.0 [32] was applied to enumerate transmembrane helices with default parameter values.”
Escherichia coli K-12: a cooperatively developed annotation snapshot—2005 (2006, neutral): “20 http://www.pubmedcentral.nih.gov/ (11). 21 http://www.enzim.hu/hmmtop ( 24 ).”