ConSurf Quick Analysis Procedure
From Proteopedia
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Here is a quick procedure for coloring a protein molecule by [[Introduction to Evolutionary Conservation|evolutionary conservation]]. This procedure does not necessarily give the highest quality result, but will give you a preliminary result that is often sufficient. If you wish to take it further, see [[ConSurfDB_vs._ConSurf#Limiting_ConSurf_Analysis_to_Proteins_of_a_Single_Function|Limiting ConSurf Analysis to Proteins of a Single Function]]. | Here is a quick procedure for coloring a protein molecule by [[Introduction to Evolutionary Conservation|evolutionary conservation]]. This procedure does not necessarily give the highest quality result, but will give you a preliminary result that is often sufficient. If you wish to take it further, see [[ConSurfDB_vs._ConSurf#Limiting_ConSurf_Analysis_to_Proteins_of_a_Single_Function|Limiting ConSurf Analysis to Proteins of a Single Function]]. | ||
| - | + | <ol> | |
| - | + | <li> Go to the [http://consurf.tau.ac.il ConSurf Server]. | |
| - | + | <li> Check ''Amino Acids''. | |
| - | + | <li> Check '''Yes''' there is a known protein structure. | |
| - | + | <li> Enter your [[PDB code]] and click the ''Next'' button. | |
| - | + | <li> Choose one chain from the pull-down ''Chain Identifier'' menu. (ConSurf can only analyze [[Conservation%2C_Evolutionary#Use_Caution_When_Comparing_Conservation_of_Sequence-Different_Chains|one chain at a time]].) | |
| - | + | <br><br> | |
| - | + | ||
| + | |||
| + | <li> Check '''No''' you do not have a Multiple Sequence Alignment (MSA) to upload. | ||
| + | <li> Don't worry, you can leave all the settings that appear now at their defaults. | ||
| + | :If you want the server to return your result faster, reduce ''Maximum homologs to collect'' from 150 to 75. | ||
| + | <li> '''Enter your email address''' in the bottom slot! This avoids losing the result and having to do it over. | ||
| + | <li> Click the ''Submit'' button. | ||
| + | <li> Processing may take a few minutes or a few hours. After <font color="red">FINISHED</font> appears at the top of the '''Job Status Page''', | ||
| + | </ol> | ||
Revision as of 22:38, 6 February 2016
Here is a quick procedure for coloring a protein molecule by evolutionary conservation. This procedure does not necessarily give the highest quality result, but will give you a preliminary result that is often sufficient. If you wish to take it further, see Limiting ConSurf Analysis to Proteins of a Single Function.
- Go to the ConSurf Server.
- Check Amino Acids.
- Check Yes there is a known protein structure.
- Enter your PDB code and click the Next button.
- Choose one chain from the pull-down Chain Identifier menu. (ConSurf can only analyze one chain at a time.)
- Check No you do not have a Multiple Sequence Alignment (MSA) to upload.
- Don't worry, you can leave all the settings that appear now at their defaults.
- If you want the server to return your result faster, reduce Maximum homologs to collect from 150 to 75.
- Enter your email address in the bottom slot! This avoids losing the result and having to do it over.
- Click the Submit button.
- Processing may take a few minutes or a few hours. After FINISHED appears at the top of the Job Status Page,
