2
$\begingroup$

For my undergraduate research project, I'm trying to compare the structures of some proteins, specifically transcription factors crucial for dehydration tolerance in plants, in the hope of finding differences that make each protein more or less dehydration tolerant than the others. i want to compare the selected transcription factors at their structural level. structure of one transcription factor from different plant species such as rice,sorghum,maize etc. are considered. ultimately i'm hoping to find a relationship between these structures of proteins and their respective level of dehydration tolerance in each plant.

Is there any database or a site where I can find information regarding this?

Improve this question
$\endgroup$
6
  • 2
    $\begingroup$ Is it the proteins that are dehydration tolerant or the plants? Are you looking for a database of protein or plant features? And are you interested in the transcription factors or in the protein products of the genes regulated by the transcription factors? Please edit your question and explain what you are trying to do in more detail and tell us what you have so far. $\endgroup$
    – terdon ♦
    Oct 19, 2017 at 9:42
  • $\begingroup$ i'm not looking for a database of plant features. hoping to find more information regarding the comparison of protein structures. thank you! $\endgroup$
    – Loch23
    Oct 19, 2017 at 10:29
  • $\begingroup$ So you want to compare the structures of the transcription factors? Do you have a list of proteins of interest? Have you checked if they have known structures? Will you need to predict the structures? Have you looked at any structural alignment tools? More importantly, what makes you think the structures of the transcription factors will be relevant here? This sounds very much like an XY problem. $\endgroup$
    – terdon ♦
    Oct 19, 2017 at 10:34
  • $\begingroup$ This project is done both in the protein sequence level and the structural level. I'm curious whether the plants with different levels of dehydration tolerance is maybe caused by the differences of responsible proteins at their structural level $\endgroup$
    – Loch23
    Oct 20, 2017 at 3:25
  • $\begingroup$ OK, but you haven't answered my questions and we need the answers to be able to help. Do you have a specific list of proteins of interest and do you know if those proteins have known structures? And, again, it doesn't make much sense to be looking at the structure of the TFs, you should instead look at the structures of the protein products of the genes controlled by the TFs. The structure of the TFs will represent their function as transcription factors. $\endgroup$
    – terdon ♦
    Oct 20, 2017 at 8:43

1 Answer 1

Reset to default
1
$\begingroup$

Have you explored in PDB?. If you already have a starting sequence, you can use it as input to search with phmmer using PDB as database. Once you have a curated set to analyse, you can visualize and align the structures with VMD, for example.

Improve this answer
$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge that you have read and understand our privacy policy and code of conduct.

Not the answer you're looking for? Browse other questions tagged or ask your own question.