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), ~~salt bridged residues are less conserved than average. With~~ a custom ConSurf Server result APD 0.91, the salt-bridged residues ~~rise to~~ average conservation. With a custom result APD 0.48, the between-chain salt bridges have above-average conservation (7.6 vs. 6.2), 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.'''

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).

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), salt bridged residues are less conserved than average. With a custom ConSurf Server result APD 0.91, the salt-bridged residues rise to average conservation. With a custom result APD 0.48, the between-chain salt bridges have above-average conservation (7.6 vs. 6.2), 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.'''
+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).
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