Currently I'm working on a bioinformatics project in which I'm trying to predict the function of an uncharacterized honey bee protein by comparing it to other known proteins. The query protein I have shows in BLAST that its sequence is very similar to dorsal-ventral patterning proteins of other insects, so I want to compare my protein to these known proteins to estimate/evaluate its possible function.
My problem is that most programs require a PDB code for analysis. Is there any program/tool out there that compares an unknown protein structure to known ones? How should I go about this?
Homology modeling. https://en.wikipedia.org/wiki/Homology_modeling
Classification of Hypothetical or uncharacterized proteins can be done through pfam and svmprot server.
Enter ur uncharacterized protein sequence (fasta) in the search box and the server will predict the family and function of that sequence. Thus u may get an idea whether the fuctions of uncharacterized protein meet ur criteria or not.
https://pfam.xfam.org
http://bidd2.nus.edu.sg/cgi-bin/svmprot/svmprot.cgi
Bayesian approach may be taken to assign a probability for a hypothetical protein to display the annotated function.
Thank you, these are very helpful. Although, if anybody knows one, I was also looking for a specific program that could analyze the unknown protein with a set of chosen, known, similar sequences/proteins by overlaying the structure/domains for example, or something similar.
Dear Haley,
Perhaps the following is what you're looking for:
Use I-Tasser
https://zhanglab.ccmb.med.umich.edu/I-TASSER/
This is a 3-D prediction program. It gives you an idea how your unknown protein looks like (an some idea which proteins resembles yours), but more importantly for you: it gives you a pdb format of your protein that can be used further.
Hope this is of any help to you.
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