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Protocols

TM Finder specifications

Information


Unique identifier OMICS_23464
Name TM Finder
Alternative name TM-Finder
Software type Application/Script
Interface Web user interface
Restrictions to use None
Input data A protein sequence.
Input format SWISS-PROT
Output data Some TM segments based on the combined prediction from hydrophobicity and helicity.
Programming languages C, Perl
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Charles Deber

Publication for TM Finder

TM Finder citations

 (7)
call_split

A Motif in the F Homomorph of Rabbit Haemorrhagic Disease Virus Polymerase Is Important for the Subcellular Localisation of the Protein and Its Ability to Induce Redistribution of Golgi Membranes

2017
Viruses
PMCID: 5580459
PMID: 28763035
DOI: 10.3390/v9080202
call_split See protocol

[…] Kyte–Doolittle hydrophobicity plots [], MPex [], TM Finder [] and TMpred [] prediction programs were used for identification of a putative interacting motif.Graphs were generated using GraphPad Prism software (La Jolla, CA, USA; http://www.graphpad. […]

library_books

Computational Approaches for Revealing the Structure of Membrane Transporters: Case Study on Bilitranslocase

2017
Comput Struct Biotechnol J
PMCID: 5312651
PMID: 28228927
DOI: 10.1016/j.csbj.2017.01.008

[…] ed on hydrophobicity indexes , , and several hydropathy analyses that identify long stretches of hydrophobic residues are available for the topology prediction of TM helices (KD , PRED-TMR , SOSUI , TM Finder , TopPred2 ) or barrels (BBF , BOMP ). These methods are successful at identifying the hydrophobic core of TM regions, but cannot precisely determine the ends of TM residues, therefore they […]

library_books

The Peptidoglycan Binding Protein SjcF1 Influences Septal Junction Function and Channel Formation in the Filamentous Cyanobacterium Anabaena

2015
MBio
PMCID: 4488944
PMID: 26126850
DOI: 10.1128/mBio.00376-15

[…] 3 helical TM [see  in the supplemental material]), FraD (5 TM [see ]), SjcF1 (1 TM [see ]), and SepJ (9 TM [see ]). The programs used are DAS (), MEMSAT (), TM-Pred (), SOSUI (), SPLIT (), Minnou (), TM-Finder (), TopCon (), PHDhtm (), and TMHMM (). […]

library_books

A Knockout Mutation of a Constitutive GPCR in Tetrahymena Decreases Both G Protein Activity and Chemoattraction

2011
PLoS One
PMCID: 3226668
PMID: 22140501
DOI: 10.1371/journal.pone.0028022

[…] Gpcr6p was then used to predict possible structure and function. The consensus seven membrane spanning regions of Gpcr6p were derived from several available tools: TMPRED , Top-Pred II , TMHMM 2.0 , TM Finder . […]

library_books

Identification of Calcium Independent and Calcium Enhanced Binding between S100B and the Dopamine D2 Receptor

2011
Biochemistry
PMCID: 3196243
PMID: 21932834
DOI: 10.1021/bi201054x

[…] esidues R217-Q345 (IC3) from the D2S dopamine receptor was a generous gift from K. Neve (Oregon Health and Science University, Portland, OR).() This region, containing the entire IC3 as identified by TM-Finder,() was moved into a p11 plasmid (Structural Genomics Consortium-Toronto) containing a TEV protease cleavable His6 purification tag. A synthetic gene construct covering residues S288-Q345 of […]

library_books

Identification of the pollen self incompatibility determinant in Papaver rhoeas

2009
Nature
PMCID: 2699350
PMID: 19483678
DOI: 10.1038/nature08027

[…] We analysed PrpS sequences using a number of protein prediction programmes: TMHMM2.0, PredictProtein, SOSUI, HMMTOP, TMpred, TM-Finder, SPLIT 4, ConPredII, Phobius. TMHMM2.0 in particular, is regarded as a very robust transmembrane helix predictor, though predicting the number of membrane-spanning regions remains difficult. […]

Citations

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TM Finder institution(s)
Division of Structural Biology and Biochemistry, Research Institute, Hospital for Sick Children, Toronto, ON, Canada; Bioinformatics Supercomputing Centre, Research Institute, Hospital for Sick Children, Toronto, ON, Canada; Department of Biochemistry, University of Toronto, Toronto, ON, Canada
TM Finder funding source(s)
Supported by grants from the Natural Sciences and Engineering Research Council of Canada, the Canadian Institutes of Health Research, and the Research Training Committee at the Hospital for Sick Children.

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