I retrieved a sequence of a receptor protein from Uniprot, and am currently using PSIPRED, TMHMM and Uniprot to compare their transmembrane (TM) predictions of the protein. But I want to ensure if they are considered among the best/reliable TM prediction sites. Hence my question. I would like to know what tools you think are the best. I am ready to consider 5 of the best ones for comparison. Thanks
Dear Dheeraj,
As you 'requested' a top 5 of best tools (besides the one you already used).
1. TOPCONS (my personal favourite)
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4489233/
and the description of the update:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4489233/
and a version to examine one single sequence:
https://academic.oup.com/bioinformatics/article/27/9/1322/242605
2. SCAMPI2: an improved version of SCAMPI
https://academic.oup.com/bioinformatics/article/32/8/1158/1743866
The authors have an interesting remark regarding TMHMM you used! I quote: “Finally, we found it interestingly that the method that is best at separating TM and non-TM proteins is the 15-years-old TMHMM, with 99% accuracy. However, the good separation comes at the price of non-optimal accurate topology predictions. The accuracy is 56 versus 63% for HMMTOP developed at the same time.”
3. MEMSAT3:
https://academic.oup.com/bioinformatics/article/23/5/538/239106
4. Heliquest combined with Heliquest based Eisenberg plot approach: If you want to use an “out of the box” approach you can use Heliquest. See the following reference for an example on how this works out:
Article Prediction of Lipid-Binding Regions in Cytoplasmic and Extra...
And the corresponding supplement for more details:
https://www.researchgate.net/publication/328346727_SupplJMemBiol2013pdf
5. PRED-TMBB2: (suitable for beta-barrel outer membrane proteins)
https://academic.oup.com/bioinformatics/article/32/17/i665/2450774
Wishing you all the best with your research in this exciting field.
- Badges
- Science topic
- Similar topics
- Cognitive Science
- Thinking