Actually, i would like to predict the transmembrane region in several membrane proteins. I have tried several online software's including TMpred, MEMSAT, PROTTER, HMMTOP, TMHMM and DAS. I have got different results from each software. For example i have predicted TM helix for protein WelM and got the results as follows
TMpred - 2 helices,
MEMSAT - 2 helices (Figure attached)
PROTTER - no helices (Figure attached),
HMMTOP- no helices,
TMHMM- no helices,
DAS- 3 helices
Im so confused about the results, anyone can suggest me the trustworthy software.
Probably you can reference some articles which are benchmarking the tools.
http://onlinelibrary.wiley.com/doi/10.1002/prot.24749/full
You can use DG Predictor http://dgpred.cbr.su.se/ that is based on a biologically determined hydrophobicity scale. But in the end a wet experiment should be done to confirm any prediction.
You could use CCTOP http://cctop.enzim.ttk.mta.hu/
It creates a consensus topology of several prediction methods adding constaints from experiments as well. You can turn off TM filter if you are sure that your protein is transmembrane.
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