ConSurfDB vs. ConSurf: Difference between revisions

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Eric Martz (talk | contribs)
ConfirmAccount, Editor, Print3D, Tester, Bureaucrats, journal, Administrators
30,128 edits
Eric Martz (talk | contribs)
ConfirmAccount, Editor, Print3D, Tester, Bureaucrats, journal, Administrators
30,128 edits
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#Under ''Maximum Homologs to collect'', change 50 to '''all'''. The other options in this section can be left at their default settings.
#Under ''Maximum Homologs to collect'', change 50 to '''all'''. The other options in this section can be left at their default settings.
#Enter your email address and click the ''Submit'' button.
#Enter your email address and click the ''Submit'' button.
#When the job is completed, under ''Running Messages'', note the number of unique sequences used in the calculation.
#After a few minutes, a red message will appear "Please choose which sequences you want to use for ConSurf calculation". However, this message '''may appear low on the page, out of view''', so scroll down periodically to check for it. The job cannot continue until you select the sequences.
#Under ''Final Results'', ''Sequences'', click on ''Unique Sequences Used''.
#Scan the names of the proteins in the list that has checkboxes, under the header "Sequences producing significant alignments:". Find the first case where the function of the protein is not the same as the protein of interest (or the function is unclear). Usually you will want to exclude sequences for proteins of different functions.
#Looking down the list of sequences from the top, find where the function of the protein first differs from that of the query protein of interest. Note  the number of the last sequence with the same function as the query protein. We'll call this the '''max with same function''' number.
#Scroll to the bottom of the page and put the number of the last sequence having the same function as the protein of interest in the box "Select the first [ .... ] sequences". Then click on the "Update selection" button.
#Re-run your ConSurf job making only one change. Set the ''Max. Number of Homologues'' to the "max with same function" that you determined in the previous step.
#Scroll back to the top and make sure that only the desired sequences are checked. (Of course you may check or uncheck individual sequences if you wish.)
#When you are satisfied, scroll back to the bottom of the sequences list and click the ''Submit'' button.


The results of the final step above may enable you to identify more functional sites than did the ConSurf-DB result built into Proteopedia.
The results of the final step above may enable you to identify more functional sites than did the ConSurf-DB result built into Proteopedia.
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