What’s the answer? (Functional regions of proteins)

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Question of the week:

Identifying functional regions of proteins

I am studying mammalian proteins and interested to analyze the surface conservation and functionally important residues. Presently, I am using Consurf but it generates redundant result as it depends on multiple sequence alignment (When I take all the sequences, important residues might be shadwed and if I take fewer seqeunces, majority of the residues are conserved). In addition, there is no any option to select only mammalian proteins in this program, because I want to ignoresequences from bacterial as well as amphibians and reptiles’ . As my working set contains about 75 proteins I do not want to make alignments taking only relevant mamalian proteins and then fetch it to the server. I would like to know if there are better programs than consurf that would help my task easier and make my analysis more noise free. I would appreciate your suggestions and ideas.

Kisun

There were some requests for clarification of the issues, but there were also some good suggestions for modifications with the method Kisun was using and additional options with other tools as well–such as Pfam and Prosite. There was no selected answer at the time I write this, but you can check out the full discussion over there–and do contribute if you have some thoughts on it!