FirstGlance/Visualizing Conservation - Revision history

Eric Martz: /* Isopeptide-Linked Ubiquitin Trimer */

2024-07-18T18:36:36Z

Isopeptide-Linked Ubiquitin Trimer

← Older revision		Revision as of 18:36, 18 July 2024
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	An example is isopeptide bond-linked chains of ubiquitin. [[7cap]] is an isopeptide-linked trimer of ubiquitin. The carboxy-terminal Gly76 forms an isopeptide bond with Lys48. Here is one ConSurf result (300 sequences in the multiple sequence alignment (MSA), sampled from 10,122 unique similar sequences. The MSA had an [[Interpreting_ConSurf_Results#Average_Pairwise_Distance\|average pairwise distance]] of 1.15):		An example is isopeptide bond-linked chains of ubiquitin. [[7cap]] is an isopeptide-linked trimer of ubiquitin. The carboxy-terminal Gly76 forms an isopeptide bond with Lys48. Here is one ConSurf result (300 sequences in the multiple sequence alignment (MSA), sampled from 10,122 unique similar sequences. The MSA had an [[Interpreting_ConSurf_Results#Average_Pairwise_Distance\|average pairwise distance]] of 1.15):

	:[http://firstglance.jmol.org/fg.htm?mol=7cap_consurf1639680092_pipe.pdb 7CAP Conservation in ~~the latest~~ FirstGlance] ~~(Right Click, Open Link in New Tab)~~		:[http://firstglance.jmol.org/fg.htm?mol=7cap_consurf1639680092_pipe.pdb 7CAP Conservation in FirstGlance]

	First, follow the [[FirstGlance/Evaluating_Protein_Crosslinks#Instructions_for_an_Isopeptide_Bond\|instructions for getting a list of the isopeptide crosslinks]].		First, follow the [[FirstGlance/Evaluating_Protein_Crosslinks#Instructions_for_an_Isopeptide_Bond\|instructions for getting a list of the isopeptide crosslinks]].

Eric Martz: /* All Tryptophans */

2024-07-18T18:34:35Z

All Tryptophans

← Older revision		Revision as of 18:34, 18 July 2024
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	and Astrid Walrant. ''Crystals'', 2021, '''11'''(9), 1032; [https://doi.org/10.3390/cryst11091032 doi.org/10.3390/cryst11091032].</ref>. Let's see which Trps are conserved in the potassium channel [[1bl8]] (a [[Nobel_Prizes_for_3D_Molecular_Structure#2000-2009\|Nobel Prize-winning structure]]!).		and Astrid Walrant. ''Crystals'', 2021, '''11'''(9), 1032; [https://doi.org/10.3390/cryst11091032 doi.org/10.3390/cryst11091032].</ref>. Let's see which Trps are conserved in the potassium channel [[1bl8]] (a [[Nobel_Prizes_for_3D_Molecular_Structure#2000-2009\|Nobel Prize-winning structure]]!).

	:[http://firstglance.jmol.org/fg.htm?mol=1bl8_consurf1640894833_pipe.pdb Display 1BL8 ConSurf Result ~~in the latest~~ FirstGlance] ~~(Right Click, Open Link in New Tab)~~		:[http://firstglance.jmol.org/fg.htm?mol=1bl8_consurf1640894833_pipe.pdb Display 1BL8 ConSurf Result FirstGlance]

	<table class="wikitable"><tr><td colspan=3><center>		<table class="wikitable"><tr><td colspan=3><center>

Eric Martz: /* Conservation of Residues Binding Ligand/Substrate */

2024-07-18T18:30:19Z

Conservation of Residues Binding Ligand/Substrate

← Older revision		Revision as of 18:30, 18 July 2024
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	FirstGlance provides an easy and powerful tool to explore residues contacting any specified portion of the model. For this example, we'll use [[acetylcholinesterase]] complexed to the [https://en.wikipedia.org/wiki/VX_(nerve_agent) inhibitor VX], crystal structure [[6cqz]].		FirstGlance provides an easy and powerful tool to explore residues contacting any specified portion of the model. For this example, we'll use [[acetylcholinesterase]] complexed to the [https://en.wikipedia.org/wiki/VX_(nerve_agent) inhibitor VX], crystal structure [[6cqz]].

	:[http://firstglance.jmol.org/fg.htm?mol=6cqz_consurf1641072297_pipe.pdb Display 6CQZ ConSurf Result in ~~the latest~~ FirstGlance] ~~(Right Click, Open Link in New Tab)~~		:[http://firstglance.jmol.org/fg.htm?mol=6cqz_consurf1641072297_pipe.pdb Display 6CQZ ConSurf Result in FirstGlance]

	We'll look at the conservation of the residues that contact the ligand/inhibitor VX. From the ''ConSurf View'', go to the FirstGlance Control Panel.		We'll look at the conservation of the residues that contact the ligand/inhibitor VX. From the ''ConSurf View'', go to the FirstGlance Control Panel.

Eric Martz: /* Color by Conservation */

2024-07-18T18:28:42Z

Color by Conservation

← Older revision		Revision as of 18:28, 18 July 2024
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	===Color by Conservation===		===Color by Conservation===
	To see how well the salt-bridged residues are conserved, click the checkbox ''ConSurf Colors'' (red arrow below). Declutter the view by unchecking ''Show Backbones'' (green arrow below).		To see how well the salt-bridged residues are conserved, click the checkbox ''ConSurf Colors'' (red arrow below). Declutter the view by unchecking ''Show Backbones'' (green arrow below). Scroll down in the lower left panel and click {{Yelspan\|List All}} to get a spreadsheet-ready list that includes conservation values for each pair of salt-bridged atoms.
	<br>		<br>
	<table class="wikitable"><tr><td>		<table class="wikitable"><tr><td>

Eric Martz: /* Go To The FirstGlance Control Panel */

2024-07-18T18:21:22Z

Go To The FirstGlance Control Panel

← Older revision		Revision as of 18:21, 18 July 2024
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	To further explore the pattern of conservation, we need to change from the ''ConSurf View'' to the ''FirstGlance Control Panel''. Click the link indicated by the red arrow in the above snapshot.		To further explore the pattern of conservation, we need to change from the ''ConSurf View'' to the ''FirstGlance Control Panel''. Click the link indicated by the red arrow in the above snapshot.

	The ''FirstGlance Control Panel'' has 5 tabs (see snapshot ~~in the next section~~). The ''Molecule Information Tab'' and the ''Views'' tab each provide a wealth of information.		The ''FirstGlance Control Panel'' has 5 tabs (see snapshot at right). The ''Molecule Information Tab'' and the ''Views'' tab each provide a wealth of information.

	Notice that you can move freely back and forth between the ''ConSurf Controls'' and the ''FirstGlance Controls'' using the link '''ConSurf Controls''' in the middle of the left side of FirstGlance.		Notice that you can move freely back and forth between the ''ConSurf Controls'' and the ''FirstGlance Controls'' using the link '''ConSurf Controls''' in the middle of the left side of FirstGlance.

Eric Martz: /* Optimization */

2024-07-18T18:19:25Z

Optimization

← Older revision		Revision as of 18:19, 18 July 2024
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	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 (see [https://pdb101.rcsb.org/motm/242 Coronavirus Proteases]).		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 (see [https://pdb101.rcsb.org/motm/242 Coronavirus Proteases]).

	:[http://firstglance.jmol.org/fg.htm?mol=7bak_consurf1641000454_pipe.pdb Display 7BAK ConSurf Result in FirstGlance] ~~(Right click, Open Link in New Tab.)~~		:[http://firstglance.jmol.org/fg.htm?mol=7bak_consurf1641000454_pipe.pdb Display 7BAK ConSurf Result in FirstGlance]

	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 ([[Interpreting_ConSurf_Results#Average_Pairwise_Distance\|average pairwise distance]] 0.34), leaving conservation grades 2 and 3 almost unoccupied. These inadequacies are highlighted by a distribution report displayed by FirstGlance.		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 ([[Interpreting_ConSurf_Results#Average_Pairwise_Distance\|average pairwise distance]] 0.34), leaving conservation grades 2 and 3 almost unoccupied. These inadequacies are highlighted by a distribution report displayed by FirstGlance.

Eric Martz: /* Optimization */

2024-07-18T18:18:20Z

Optimization

← Older revision		Revision as of 18:18, 18 July 2024
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	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 (see [https://pdb101.rcsb.org/motm/242 Coronavirus Proteases]).		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 (see [https://pdb101.rcsb.org/motm/242 Coronavirus Proteases]).

	:[http://firstglance.jmol.org/fg.htm?mol=7bak_consurf1641000454_pipe.pdb Display 7BAK ConSurf Result in FirstGlance ~~3.8~~] (Right click, Open Link in New Tab.)		:[http://firstglance.jmol.org/fg.htm?mol=7bak_consurf1641000454_pipe.pdb Display 7BAK ConSurf Result in FirstGlance] (Right click, Open Link in New Tab.)

	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 ([[Interpreting_ConSurf_Results#Average_Pairwise_Distance\|average pairwise distance]] 0.34), leaving conservation grades 2 and 3 almost unoccupied. These inadequacies are highlighted by a distribution report displayed by FirstGlance.		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 ([[Interpreting_ConSurf_Results#Average_Pairwise_Distance\|average pairwise distance]] 0.34), leaving conservation grades 2 and 3 almost unoccupied. These inadequacies are highlighted by a distribution report displayed by FirstGlance.

Eric Martz at 18:16, 18 July 2024

2024-07-18T18:16:14Z

← Older revision		Revision as of 18:16, 18 July 2024
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	There are 2 ways to analyzie your own ConSurf Server results in FirstGlance:		There are 2 ways to analyzie your own ConSurf Server results in FirstGlance:
	:1. At the ConSurf Server results page, open ''High Resolution Figures and PDB Files'', and then click ''Download ConSurf PDB File for FirstGlance in Jmol''. ~~Then~~ [http://~~www~~.~~bioinformatics~~.org~~/firstglance/fgij~~/where.htm#u upload the downloaded file to FirstGlance]. By downloading the PDB file, you will have it after the results '''disappear''' from the ConSurf Server.		:1. At the ConSurf Server results page, open ''High Resolution Figures and PDB Files'', and then click ''Download ConSurf PDB File for FirstGlance in Jmol''. Now, you can [http://firstglance.jmol.org/where.htm#u upload the downloaded file to FirstGlance]. By downloading the PDB file, you will have it after the results '''disappear''' from the ConSurf Server.

	:2. At the ConSurf results page, ~~under the heading~~ ''~~PDB Files~~''~~, right~~ click on ''PDB File ~~with ConSurf Results in its Header,~~ for FirstGlance in Jmol'' and select '''Copy Link ~~Address~~'''. Then, at FirstGlance, click [http://~~www~~.~~bioinformatics~~.org~~/firstglance/fgij~~/where.htm#u enter a molecule's URL], paste the address into the slot, and click Submit.		:2. At the ConSurf results page, '''Right''' click the link ''Download ConSurf PDB File for FirstGlance in Jmol'', and select '''Copy Link'''. Then, at FirstGlance, click [http://firstglance.jmol.org/where.htm#u enter a molecule's URL], paste the address into the slot, and click Submit.

Eric Martz at 18:12, 18 July 2024

2024-07-18T18:12:30Z

← Older revision		Revision as of 18:12, 18 July 2024
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	There are 2 ways to analyzie your own ConSurf Server results in FirstGlance:		There are 2 ways to analyzie your own ConSurf Server results in FirstGlance:
	:1. At the ConSurf Server results page, ''~~'download the~~ PDB ~~file~~''~~' by clicking~~ ''PDB File ~~with ConSurf Results in its Header,~~ for FirstGlance in Jmol''. Then [http://www.bioinformatics.org/firstglance/fgij/where.htm#u upload it to FirstGlance]. By downloading the PDB file, you will have it after the results '''disappear''' from the ConSurf Server.		:1. At the ConSurf Server results page, open ''High Resolution Figures and PDB Files'', and then click ''Download ConSurf PDB File for FirstGlance in Jmol''. Then [http://www.bioinformatics.org/firstglance/fgij/where.htm#u upload the downloaded file to FirstGlance]. By downloading the PDB file, you will have it after the results '''disappear''' from the ConSurf Server.

	:2. At the ConSurf results page, under the heading ''PDB Files'', right click on ''PDB File with ConSurf Results in its Header, for FirstGlance in Jmol'' and select '''Copy Link Address'''. Then, at FirstGlance, click [http://www.bioinformatics.org/firstglance/fgij/where.htm#u enter a molecule's URL], paste the address into the slot, and click Submit.		:2. At the ConSurf results page, under the heading ''PDB Files'', right click on ''PDB File with ConSurf Results in its Header, for FirstGlance in Jmol'' and select '''Copy Link Address'''. Then, at FirstGlance, click [http://www.bioinformatics.org/firstglance/fgij/where.htm#u enter a molecule's URL], paste the address into the slot, and click Submit.

Eric Martz at 18:08, 18 July 2024

2024-07-18T18:08:40Z

← Older revision		Revision as of 18:08, 18 July 2024
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	There are 2 ways to analyzie your own ConSurf Server results in FirstGlance:		There are 2 ways to analyzie your own ConSurf Server results in FirstGlance:
	:1. At the ConSurf results page, '''download the PDB file''' by clicking ''PDB File with ConSurf Results in its Header, for FirstGlance in Jmol''. Then [http://www.bioinformatics.org/firstglance/fgij/where.htm#u upload it to FirstGlance]. By downloading the PDB file, you will have it after the results '''disappear''' from the ConSurf Server.		:1. At the ConSurf Server results page, '''download the PDB file''' by clicking ''PDB File with ConSurf Results in its Header, for FirstGlance in Jmol''. Then [http://www.bioinformatics.org/firstglance/fgij/where.htm#u upload it to FirstGlance]. By downloading the PDB file, you will have it after the results '''disappear''' from the ConSurf Server.

	:2. At the ConSurf results page, under the heading ''PDB Files'', right click on ''PDB File with ConSurf Results in its Header, for FirstGlance in Jmol'' and select '''Copy Link Address'''. Then, at FirstGlance, click [http://www.bioinformatics.org/firstglance/fgij/where.htm#u enter a molecule's URL], paste the address into the slot, and click Submit.		:2. At the ConSurf results page, under the heading ''PDB Files'', right click on ''PDB File with ConSurf Results in its Header, for FirstGlance in Jmol'' and select '''Copy Link Address'''. Then, at FirstGlance, click [http://www.bioinformatics.org/firstglance/fgij/where.htm#u enter a molecule's URL], paste the address into the slot, and click Submit.