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Below are listed pages in Proteopedia about evolutionary conservation, how to use the [http://consurf.tau.ac.il ConSurf Server], and how to interpret its results to identify functional sites in proteins. | Below are listed pages in Proteopedia about evolutionary conservation, how to use the [http://consurf.tau.ac.il ConSurf Server], and how to interpret its results to identify functional sites in proteins. | ||
==Principles== | ==Principles== | ||
* [[Introduction to Evolutionary Conservation]]: an explanation starting at the beginning, with examples. | * [[Introduction to Evolutionary Conservation]] (81K*): an explanation starting at the beginning, with examples. | ||
* [[Conservation, Evolutionary]] covers | * [[Conservation, Evolutionary]] (128K*) covers | ||
** How to locate conserved and variable patches | ** How to locate conserved and variable patches | ||
** Conservation expected to support folding of domains | ** Conservation expected to support folding of domains | ||
| Line 15: | Line 15: | ||
==Practical== | ==Practical== | ||
* [[How to see conserved regions]] lists options and how to get started. | * There are [http://firstglance.jmol.org/notes.htm#consurffg many advantages] of using FirstGlance in Jmol to visualize and analyze conservation patterns from the ConSurf Server. | ||
* [[ConSurf Quick Analysis Procedure]]: step by step for submitting a job to ConSurf. | * [[How to see conserved regions]] (18K*) lists options and how to get started. | ||
* [[ConSurfDB vs. ConSurf]] | * [[ConSurf Quick Analysis Procedure]] (9K*): step by step for submitting a job to ConSurf. | ||
* [[FirstGlance/Visualizing Conservation]] [[Image:New yellow1.gif]] January, 2022. | * [[ConSurfDB vs. ConSurf]] (37K*) Explains how to discover key conserved residues by using ConSurf settings that limit the multiple sequence alignment to proteins with the same function as the query, with illustrated cases. ConSurf results based on default settings often obscure conservation specific to the function of the protein. Also summarizes the mechanisms of the ConSurf Server and the ConSurf Database. | ||
* [[Interpreting ConSurf Results]] [[Image:New yellow1.gif]] January, 2022. | |||
* [[Help:How to Insert a ConSurf Result Into a Proteopedia Green Link]] | |||
* [[FirstGlance/Visualizing Conservation]] [[Image:New yellow1.gif]] January, 2022 (5K*). Demonstrates the conveniences offered by FirstGlance for easily seeing conservation of [[salt bridges]], [[cation-pi interactions]], residues that bind ligand, substrate, or inhibitor, residues in covalent protein crosslinks, or any residues that you specify. | |||
* [[Interpreting ConSurf Results]] [[Image:New yellow1.gif]] January, 2022 (3K*). How to tell whether a ConSurf result is optimal. | |||
* [[Help:How to Insert a ConSurf Result Into a Proteopedia Green Link]] (5K*) | |||
===Page Views=== | |||
[[Image:Asteriskinline.png]] K* (kilo) numbers in parentheses are the numbers of page views as of July, 2024. | |||
==See Also== | ==See Also== | ||
*[[Index pages]] | *[[Index pages]] | ||
Latest revision as of 02:24, 30 July 2024
The ConSurf Server, a project led by Nir Ben-Tal and Tal Pupko (Tel-Aviv University, Israel), colors each amino acid in a protein structure by its level of evolutionary conservation. Functional sites are marked by clusters of conserved surface residues. Available since 2002 and constantly upgraded, all methods are documented and its algorithms are published in peer-reviewed journals. When the confidence interval around a conservation grade is too wide, ConSurf assigns that residue a yellow color for "insufficient data".
For some quick examples, see Introduction to Evolutionary Conservation.
Below are listed pages in Proteopedia about evolutionary conservation, how to use the ConSurf Server, and how to interpret its results to identify functional sites in proteins.
PrinciplesPrinciples
- Introduction to Evolutionary Conservation (81K*): an explanation starting at the beginning, with examples.
- Conservation, Evolutionary (128K*) covers
- How to locate conserved and variable patches
- Conservation expected to support folding of domains
- Unrelated sequences in the MSA obscure functional sites, re: ConSurfDB
- Comparing sequence-different chains
- Drift in results over time due to database growth
- Other evolutionary conservation servers besides ConSurf
PracticalPractical
- There are many advantages of using FirstGlance in Jmol to visualize and analyze conservation patterns from the ConSurf Server.
- How to see conserved regions (18K*) lists options and how to get started.
- ConSurf Quick Analysis Procedure (9K*): step by step for submitting a job to ConSurf.
- ConSurfDB vs. ConSurf (37K*) Explains how to discover key conserved residues by using ConSurf settings that limit the multiple sequence alignment to proteins with the same function as the query, with illustrated cases. ConSurf results based on default settings often obscure conservation specific to the function of the protein. Also summarizes the mechanisms of the ConSurf Server and the ConSurf Database.
- FirstGlance/Visualizing Conservation
January, 2022 (5K*). Demonstrates the conveniences offered by FirstGlance for easily seeing conservation of salt bridges, cation-pi interactions, residues that bind ligand, substrate, or inhibitor, residues in covalent protein crosslinks, or any residues that you specify.
- Interpreting ConSurf Results January, 2022 (3K*). How to tell whether a ConSurf result is optimal.
Page ViewsPage Views
File:Asteriskinline.png K* (kilo) numbers in parentheses are the numbers of page views as of July, 2024.
