This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.
Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.
Interpreting ConSurf Results
From Proteopedia
| Line 1: | Line 1: | ||
This page discusses how to decide whether a [http://consurf.tau.ac.il ConSurf] result is optimal for the questions you wish to ask about a protein. It assumes that you already have one or more completed ConSurf results. For background principles and instructions on how to get a ConSurf result, please see [[ConSurf/Index]]. | This page discusses how to decide whether a [http://consurf.tau.ac.il ConSurf] result is optimal for the questions you wish to ask about a protein. It assumes that you already have one or more completed ConSurf results. For background principles and instructions on how to get a ConSurf result, please see [[ConSurf/Index]]. | ||
| - | A ConSurf result depends crucially on the sequences included in the multiple sequence alignment (MSA). The optimal breadth of coverage of those sequences depends on your goal. | + | ==Breadth of the MSA== |
| + | A ConSurf result depends crucially on the sequences included in the multiple sequence alignment (MSA). The optimal breadth of coverage of those sequences depends on your goal. The breadth of an MSA is represented in the [[#Average Pairwise Distance]] (APD). | ||
*If you want to know which residues are important for the '''specific function of one protein''', then the MSA should not include proteins with different functions. See [[ConSurfDB_vs._ConSurf#Limiting_ConSurf_Analysis_to_Proteins_of_a_Single_Function|Limiting ConSurf Analysis to Proteins of a Single Function]]. | *If you want to know which residues are important for the '''specific function of one protein''', then the MSA should not include proteins with different functions. See [[ConSurfDB_vs._ConSurf#Limiting_ConSurf_Analysis_to_Proteins_of_a_Single_Function|Limiting ConSurf Analysis to Proteins of a Single Function]]. | ||
*If you want to know which residues remain important throughout a protein family (or superfamily), then the MSA should be broad enough to include representives of the entire family. Such an MSA may obscure conservation of some residues important for a specific function. | *If you want to know which residues remain important throughout a protein family (or superfamily), then the MSA should be broad enough to include representives of the entire family. Such an MSA may obscure conservation of some residues important for a specific function. | ||
For more about this, see [https://consurf.tau.ac.il/faq.php#q13 What is the best way to collect homologous sequences in order to construct an MSA?] at the ConSurf Server. | For more about this, see [https://consurf.tau.ac.il/faq.php#q13 What is the best way to collect homologous sequences in order to construct an MSA?] at the ConSurf Server. | ||
Revision as of 23:15, 23 December 2021
This page discusses how to decide whether a ConSurf result is optimal for the questions you wish to ask about a protein. It assumes that you already have one or more completed ConSurf results. For background principles and instructions on how to get a ConSurf result, please see ConSurf/Index.
Breadth of the MSA
A ConSurf result depends crucially on the sequences included in the multiple sequence alignment (MSA). The optimal breadth of coverage of those sequences depends on your goal. The breadth of an MSA is represented in the #Average Pairwise Distance (APD).
- If you want to know which residues are important for the specific function of one protein, then the MSA should not include proteins with different functions. See Limiting ConSurf Analysis to Proteins of a Single Function.
- If you want to know which residues remain important throughout a protein family (or superfamily), then the MSA should be broad enough to include representives of the entire family. Such an MSA may obscure conservation of some residues important for a specific function.
For more about this, see What is the best way to collect homologous sequences in order to construct an MSA? at the ConSurf Server.
