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Protocols

TMDET specifications

Information


Unique identifier OMICS_01615
Name TMDET
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for TMDET

TMDET citations

 (10)
library_books

Statistically derived asymmetric membrane potentials from α helical and β barrel membrane proteins

2018
Sci Rep
PMCID: 5849751
PMID: 29535329
DOI: 10.1038/s41598-018-22476-6

[…] erived scoring functions to predict protein embedding in the membrane; however, lack of benchmarking data precludes extensive testing of these methods. An earlier method used by the PDBTM database is TMDET, which cuts the protein into slices and uses hydrophobicity and structural information of the Cα-trace (such as straightness, turns, and termini) to derive an objective function, which is used t […]

library_books

Alpha conotoxin BuIA globular isomer is a competitive antagonist for oleoyl L alpha lysophosphatidic acid binding to LPAR6; A molecular dynamics study

2017
PLoS One
PMCID: 5718415
PMID: 29211777
DOI: 10.1371/journal.pone.0189154

[…] comparative topological changes in the seven transmembrane segments of LPAR6 were monitored in bound and unbound systems (). These changes were predicted at 20 ns by analysing the coordinate files in TMDET. LPAR6 N-terminal region was elongated in conotoxin-bound complexes. Similarly, compression of LPAR6 C-terminal region was prominent due to binding with conotoxins as compared to apo form. Signi […]

library_books

Approaches to ab initio molecular replacement of α helical transmembrane proteins

2017
Acta Crystallogr D Struct Biol
PMCID: 5713875
PMID: 29199978
DOI: 10.1107/S2059798317016436

[…] a result of these complications, of the more than 130 000 protein structures currently deposited in the PDB (Berman et al., 2000), fewer than 3% (3084) are classified as transmembrane proteins by the TMDET algorithm (Tusnády et al., 2004). The low number of structures means that the probability of finding homologous structures to use for molecular replacement (MR) can often be low, so that the use […]

library_books

The human transmembrane proteome

2015
Biol Direct
PMCID: 4445273
PMID: 26018427
DOI: 10.1186/s13062-015-0061-x

[…] (version 1.089) databases. The most reliable data can be found in the PDBTM database [–], which contains the 3D structure of TMPs together with the most likely membrane orientation determined by the TMDET algorithm []. Because PDBTM does not contain topology information, only the sequential localizations of the TMHs, topology information was collected from the TOPDB database [].The TOPDB database […]

call_split

Membrane protein orientation and refinement using a knowledge based statistical potential

2013
BMC Bioinformatics
PMCID: 3852961
PMID: 24047460
DOI: 10.1186/1471-2105-14-276
call_split See protocol

[…] eir tilt angles determined using Attenuated Total Reflectance Fourier Transform Infrared (ATR-FTIR) spectroscopy. We assessed performance of the potential, using GA search, and 4 other methods – OPM, TMDET, Ez-3D and a potential derived from experimental measurements of free energy of membrane insertion described by Hessa et al. [] combined with a grid search - with these structures, comparing the […]

library_books

Transmembrane Protein Alignment and Fold Recognition Based on Predicted Topology

2013
PLoS One
PMCID: 3716705
PMID: 23894534
DOI: 10.1371/journal.pone.0069744

[…] The Protein Data Bank of Transmembrane Proteins (PDBTM) is the most comprehensive TMP database currently available. It uses an automated algorithm (TMDET) to identify TMPs in PDB and calculate their topology structures. Compared to peer databases , , PDBTM is convenient for large-scale testing, and updated weekly by synchronizing with PDB. Hence […]

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TMDET institution(s)
Institute of Enzymology, BRC, Hungarian Academy of Sciences, Budapest, Hungary

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