Answers.Body: <p>Have you explored in <a href="https://www.rcsb.org/pdb/home/home.do" rel="nofollow noreferrer">PDB</a>?. If you already have a starting sequence, you can use it as input to search with <a href="https://www.ebi.ac.uk/Tools/hmmer/search/phmmer" rel="nofollow noreferrer">phmmer</a> using PDB as database. Once you have a curated set to analyse, you can visualize and align the structures with <a href="http://www.ks.uiuc.edu/Research/vmd/" rel="nofollow noreferrer">VMD</a>, for example. </p>
  
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Answers.CreationDate: 2017-10-20T15:59:41.620Z
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Answers.UserDisplayName: Kraken
Body: <p>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.</p>
  
  <p>Is there any database or a site where I can find information regarding this?</p>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-10-19T09:42:31.593Z
Comments.Text: 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.
Comments.UserDisplayName: terdon
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Comments.CreationDate: 2017-10-19T10:29:49.327Z
Comments.Text: i'm not looking for a database of plant features. hoping to find more information regarding the comparison of protein structures. thank you!
Comments.UserDisplayName: Loch23
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Comments.CreationDate: 2017-10-19T10:34:23.437Z
Comments.Text: 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](http://meta.stackexchange.com/q/66377/203101).
Comments.UserDisplayName: terdon
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Comments.CreationDate: 2017-10-20T03:25:06.980Z
Comments.Text: 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
Comments.UserDisplayName: Loch23
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Comments.CreationDate: 2017-10-20T08:43:12.527Z
Comments.Text: 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.
Comments.UserDisplayName: terdon
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Comments.CreationDate: 2017-11-20T07:49:46.413Z
Comments.Text: @terdon I believe your last comment is not entirely correct, if the TF changes conformation upon drought it would be extremely important to take the structure into account.
Comments.UserDisplayName: holmrenser
Tags: <public-databases><protein-structure>
Title: How can I compare structures of proteins responsible for dehydration tolerance in plants?
ThreadText: # How can I compare structures of proteins responsible for dehydration tolerance in plants?
  
  (Asked by: username_0 on 2017-10-19)
  
  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?
  
  **Tags:** public-databases, protein-structure
  
  > **Comments:**
  > **username_1**: 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.  
  > **username_0**: i'm not looking for a database of plant features. hoping to find more information regarding the comparison of protein structures. thank you!  
  > **username_1**: 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](http://meta.stackexchange.com/q/66377/203101).  
  > **username_0**: 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  
  > **username_1**: 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.  
  > **username_2**: @username_1 I believe your last comment is not entirely correct, if the TF changes conformation upon drought it would be extremely important to take the structure into account.  
  
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  ## 1 answers
  
  ### Answer by username_3 on 2017-10-20. Score: 1
  
  Have you explored in [PDB](https://www.rcsb.org/pdb/home/home.do)?. If you already have a starting sequence, you can use it as input to search with [phmmer](https://www.ebi.ac.uk/Tools/hmmer/search/phmmer) using PDB as database. Once you have a curated set to analyse, you can visualize and align the structures with [VMD](http://www.ks.uiuc.edu/Research/vmd/), for example.
  
  
  ---
  
  