ConSurfDB vs. ConSurf: Difference between revisions

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[[FirstGlance in Jmol]] displays <scene name='39/399854/4dnw_consurf_apd-point48/2'>all salt bridges</scene> with one click (Tools tab), colored by conservation (if pre-processed by the ConSurf Server), and can list them, '''spreadsheet-ready, including conservation level numbers, and marking those between chains'''.

With the default ConSurf Server result ('''APD 1.42'''), and with a custom ConSurf Server result '''APD 0.91''', the salt-bridged residues have about '''average''' conservation. With a custom result '''APD 0.48''', the between-chain salt bridges have above-average conservation (7.6 vs. 6.8), while the within-chain salt bridges have average conservation (6.3). In conclusion, when the multiple sequence alignment is limited to sequences closely related to the query (APD 0.48), '''between-chain salt bridged residues are more conserved than are within-chain salt bridged residues.''' The difference is '''statistically significant''' (p < 0.01).

With the default ConSurf Server result '''APD 1.42''', and with a custom ConSurf Server result '''APD 0.91''', the salt-bridged residues have about '''average''' conservation. With a custom result '''APD 0.48''', the between-chain salt bridges have '''above-average''' conservation (7.6 vs. 6.8), while the within-chain salt bridges have below average conservation (6.3 vs. 6.8). In conclusion, when the multiple sequence alignment is limited to sequences closely related to the query (APD 0.48), '''between-chain salt bridged residues are more conserved than are within-chain salt bridged residues.''' The difference is '''statistically significant''' (p < 0.01<ref name="stats">With APD 0.48, mean conservation of between-chain salt bridged atoms is 7.57 ± 0.13 SEM. Subtracting 3 SEM (99% confidence limit) gives 7.18. This does not overlap with either 7.16 (the all-salt-bridged atoms mean + 3 SEM) or 6.82 (the mean for NOT between chains salt-bridged atoms + 3 SEM).</ref>).

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~~Average~~ Conservation Levels ± SEM

Mean Conservation Levels ± SEM

</center>

</td>

ConSurfDB vs. ConSurf: Difference between revisions

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@@ Line 171: / Line 171: @@
 [[FirstGlance in Jmol]] displays <scene name='39/399854/4dnw_consurf_apd-point48/2'>all salt bridges</scene> with one click (Tools tab), colored by conservation (if pre-processed by the ConSurf Server), and can list them, '''spreadsheet-ready, including conservation level numbers, and marking those between chains'''.
-With the default ConSurf Server result ('''APD 1.42'''), and with a custom ConSurf Server result '''APD 0.91''', the salt-bridged residues have about '''average''' conservation. With a custom result '''APD 0.48''', the between-chain salt bridges have above-average conservation (7.6 vs. 6.8), while the within-chain salt bridges have average conservation (6.3). In conclusion, when the multiple sequence alignment is limited to sequences closely related to the query (APD 0.48), '''between-chain salt bridged residues are more conserved than are within-chain salt bridged residues.''' The difference is '''statistically significant''' (p < 0.01).
+With the default ConSurf Server result '''APD 1.42''', and with a custom ConSurf Server result '''APD 0.91''', the salt-bridged residues have about '''average''' conservation. With a custom result '''APD 0.48''', the between-chain salt bridges have '''above-average''' conservation (7.6 vs. 6.8), while the within-chain salt bridges have below average conservation (6.3 vs. 6.8). In conclusion, when the multiple sequence alignment is limited to sequences closely related to the query (APD 0.48), '''between-chain salt bridged residues are more conserved than are within-chain salt bridged residues.''' The difference is '''statistically significant''' (p < 0.01<ref name="stats">With APD 0.48, mean conservation of between-chain salt bridged atoms is 7.57 &plusmn; 0.13 SEM. Subtracting 3 SEM (99% confidence limit) gives 7.18. This does not overlap with either 7.16 (the all-salt-bridged atoms mean + 3 SEM) or 6.82 (the mean for NOT between chains salt-bridged atoms + 3 SEM).</ref>).
 <table class="wikitable" style="text-align:center;">
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    <td colspan=3>
    <center>
-Average Conservation Levels &plusmn; SEM
+Mean Conservation Levels &plusmn; SEM
    </center>
    </td>