Sequence to structure pairwise alignment parameter tuning

[nmih]

When running QC/QA, the first thing that is done is a pairwise alignment. The quality of this alignment can have a big impact of the result. The setting of gap score and gap extend penalties should be explored to prevent bad alignments -- example to be added later..

[nmih]

Example of how small quality parameters will impact selection of representative structure.
5AQ6 has 87.5% similarity for protein b1973 chain A but does not pass quality check while 1TXL with 87% SI does, due to small differences in the alignment.

1TXL on the left and 5AQ6 on the right

[erolkavvas]

wow this is fascinating... so each representative structure (5aq6, 1tx1, ... etc) is a different strain of E. Coli? It looks like 5aq6 is BL21, 5XM5 is K12, and 1tx1 is not specified.

[nmih]

Hah yeah actually I should have looked at that too. Thanks for checking it out Erol. Actually I made a typo, it's 1txl (which is K12) not 1tx1. But the strain check should be implemented as well..