FirstGlance/Visualizing Conservation
From Proteopedia
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| + | ===Optimization=== | ||
| + | Before going further, it is good to decide whether the results are satisfactory, or need optimization. Lets consider [[7bak]], a drug-target protease of SARS-CoV-2. A ConSurf run with all default settings left 10% of the residues with insufficient data<ref name="insufficientdata">When the confidence interval for a conservation value of an amino acid is too large, ConSurf reports "insufficient data" (uncertainty: yellow color). See [https://consurf.tau.ac.il/quick_help.php#RELIABILITY Position Specific Quality] and [https://consurf.tau.ac.il/overview.php#_Toc311131298 Confidence Interval] in the ConSurf documentation.</ref> (yellow color), and the diversity in the multiple sequence alignment (MSA) was too low (average pairwise distance 0.34), leaving conservation grades 2 and 3 almost unoccupied. | ||
==Conservation of Specified Residues== | ==Conservation of Specified Residues== | ||
Revision as of 19:18, 2 January 2022
This page is under construction. It is incomplete. Eric Martz 01:22, 1 January 2022 (UTC)
FirstGlance in Jmol is the easiest-to-use tool for visualizing, understanding, and sharing protein molecular structure. It offers guided exploration with extensive explanations and examples, yet provides ample power for advanced users. With a few mouse clicks, any molecular scene can be saved as a slide presentation-ready animation (GIF file) -- see examples below, and tinyurl.com/movingmolecules.
Among many conveniences offered by FirstGlance, it is easy to see the levels of evolutionary conservation determined by ConSurf for amino acids of special interest. Below is an overview with some illustrated examples. Elsewhere you will find instructions for running ConSurf on proteins of interest.
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IMPORTANT (January, 2022): Use the unreleased beta-test version FirstGlance 3.8 Beta2 which has many improvements for ConSurf results beyond the publicly available version 3.7. Some of the features shown below are absent in version 3.7.
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Contents |
Initial View of Conservation
Initially, FirstGlance colors each amino acid in the protein chain processed by ConSurf according to its level of conservation. This gives you an overview, enabling you to see patches of highly conserved residues (functional sites).
Multiple Chains
If the model has more than one copy of the chain processed by ConSurf, you can apply conservation colors to all of those sequence-identical chains. Here, for example, is a potassium channel homotetramer:
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Optimization
Before going further, it is good to decide whether the results are satisfactory, or need optimization. Lets consider 7bak, a drug-target protease of SARS-CoV-2. A ConSurf run with all default settings left 10% of the residues with insufficient data[1] (yellow color), and the diversity in the multiple sequence alignment (MSA) was too low (average pairwise distance 0.34), leaving conservation grades 2 and 3 almost unoccupied.
Conservation of Specified Residues
Conservation of Salt Bridges & Cation-Pi Interactions
Conservation of Protein Crosslinks
See Also
References
- ↑ When the confidence interval for a conservation value of an amino acid is too large, ConSurf reports "insufficient data" (uncertainty: yellow color). See Position Specific Quality and Confidence Interval in the ConSurf documentation.
