Software: Evolutionary conservation of key amino acids more easily seen

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Software: Evolutionary conservation of key amino acids more easily seen
Submitted by Eric Martz; posted on Tuesday, January 25, 2022

FirstGlance in Jmol http://bioinformatics.org/firstglance (free and open source as always) provides guided visual exploration of macromolecular structures with remarkable ease of use (no command language needed). The "FirstGlance" it offers is maximally informative. It alerts you automatically to missing residues (quite common in X-ray crystallographic models), incomplete sidechains, and unusual components or features including unusual covalent protein crosslinks (such as thioester or lysine-cysteine NOS bonds).

Since 2006, FirstGlance has provided visualization of evolutionary conservation, calculated by the ConSurf Server http://consurf.tau.ac.il, coloring each amino acid in a protein structure by conservation level. All of ConSurf's state-of-the-art algorithms are published in peer-reviewed journals. Using ConSurf is easy. It gathers sequences, aligns them into a multiple protein sequence alignment (MSA), calculates conservation values, and colors your protein structure – all automatically. When the MSA provides inadequate information for a particular residue (large confidence interval), it is colored yellow for "insufficient data".

This new version of FirstGlance optimizes zooming in on key residues and coloring them by evolutionary conservation. "One click (or a few)" tools do this for any residues that you specify, disulfide bonds, six other kinds of covalent protein crosslinks (e.g. isopeptide bonds), all salt bridges, all cation-pi interactions, and residues contacting any ligand or other substructure that you specify. You can toggle between coloring the atoms by chemical element or evolutionary conservation, provided that the protein structure model (PDB file) has been processed by ConSurf beforehand.

Quick example for isopeptide and thioester crosslinks in FirstGlance:

Processed by ConSurf http://bioinformatics.org/firstglance/fgij/fg.htm?mol=2xi9_consurf1625260341_pipe.pdb
NOT processed by ConSurf http://bioinformatics.org/firstglance/fgij/fg.htm?mol=2xi9

Here are some illustrated practical guides:

Intro to Evolutionary Conservation: http://proteopedia.org/w/Introduction_to_Evolutionary_Conservation
ConSurf Quick Start: http://proteopedia.org/w/ConSurf_Quick_Analysis_Procedure
Is your ConSurf result optimal? (NEW) http://proteopedia.org/w/Interpreting_ConSurf_Results
Visualizing Conservation in FirstGlance (NEW): http://proteopedia.org/w/FirstGlance/Visualizing_Conservation
Using FirstGlance to distinguish genuine covalent protein crosslinks from "clashes" (NEW): http://proteopedia.org/w/FirstGlance/Evaluating_Protein_Crosslinks
Seven types of unusual protein crosslinks (NEW): http://proteopedia.org/w/Protein_crosslinks

Feedback always welcome!

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