ConSurfDB vs. ConSurf: Difference between revisions
From Proteopedia
Jump to navigationJump to search
Eric Martz (talk | contribs) |
Eric Martz (talk | contribs) |
||
| Line 164: | Line 164: | ||
[[FirstGlance in Jmol]] displays all salt bridges 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'''. | [[FirstGlance in Jmol]] displays all salt bridges 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). | 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 150 sequences closely related to the query (APD 0.48), '''between-chain salt bridged residues are more conserved than those within-chain.''' | ||
<font color="red">UPDATE IN PROGRESS:</FONT> [[User:Eric Martz|Eric Martz]] 15:02, 29 July 2024 (UTC) | <font color="red">UPDATE IN PROGRESS:</FONT> [[User:Eric Martz|Eric Martz]] 15:02, 29 July 2024 (UTC) | ||
