ConSurfDB vs. ConSurf: Difference between revisions
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====ConSurfDB==== | ====ConSurfDB==== | ||
ConSurfDB has a result (NOT SHOWN) with an '''APD of 1.63''', much higher than the APD 1.1 for the ConSurf Server with default settings. As expected, nothing in the contacts between the peptide and the groove shows high conservation in the ConSurfDB result, but Trp274 (the CD8 binding site) remains highly conserved. | ConSurfDB has a result (NOT SHOWN) with an '''APD of 1.63''', much higher than the APD 1.1 for the ConSurf Server with default settings. As expected, nothing in the contacts between the peptide and the groove shows high conservation in the ConSurfDB result, but Trp274 (the CD8 binding site) remains highly conserved. | ||
====APD 0.31==== | |||
By default, ConSurf Server excludes from the multiple sequence alignment sequences with >95% identity, or <35% identity with the query sequence. Changing those limits to >98% and <70% reduced the default APD of 1.1 to 0.31. This result shows high conservation of the following residues in the groove: | |||
* <span style="background-color:#961d54;color:white;padding-left:0.3em;padding-right:0.3em;">Level 9:</span>. | |||
**Tyr7: hydrogen bonds to the main chain oxygen of peptide amino acid 1. | |||
**Lys146: salt bridges to the carboxy terminus of the peptide. | |||
*Grade 8: | |||
**Tyr84: | |||
<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) | ||
