ConSurf/Index: Difference between revisions
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==Practical== | ==Practical== | ||
* [http://firstglance.jmol.org/notes.htm#consurffg | * 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. | ||
* [[How to see conserved regions]] lists options and how to get started. | * [[How to see conserved regions]] lists options and how to get started. | ||
* [[ConSurf Quick Analysis Procedure]]: step by step for submitting a job to ConSurf. | * [[ConSurf Quick Analysis Procedure]]: step by step for submitting a job to ConSurf. | ||
Revision as of 21:01, 18 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: an explanation starting at the beginning, with examples.
- Conservation, Evolutionary 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 lists options and how to get started.
- ConSurf Quick Analysis Procedure: step by step for submitting a job to ConSurf.
- ConSurfDB vs. ConSurf explains how each server works, and how to get the best results from each.
- FirstGlance/Visualizing Conservation
January, 2022. 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. How to tell whether a ConSurf result is optimal.