Overall report for similar proteins

PACSY-ALIGN performs multi-threaded Smith-Watermann sequence alignment with PACSY database, which is RDBMS for structural and chemical shift information of proteins. PDBSEQ_DB table is updated every months to provide most sufficient and fresh PDB data.

The ten most similar proteins from the alignment are analyzed and the brief information on them are saved in the overall report file.

* run_report.png

PACSY-ALIGN provides the overall picture of the results as a bar chart. I, H and S are 0.0 – 1.0 scale, while B is 0-100 and over 100 is represented as 100 (full bar).

I: Sequence identity

H: Sequence homology

B: Blosum62 score

S: Secondary structure agreement

* run_report.txt

* Blosum62 score

Blosum62 score is a sum of scores from Blosum62 matrix for each residue. PACSY-ALIGN uses -7 for gap opening penalty and -1 for gap extending penalty respectively. Roughly, if Blosum62 score is higher than 70, the 3D structure seems to be very similar to the user input.

* Secondary structure agreement

PACSY-ALIGN counts how many secondary structure types for residues in agreement between user input and PDB structure. It is rather insensitive when it comes to proteins with high sequence identities, however, it is useful to distinguish a similar structure protein between proteins with lower sequence identities.

* Status

It reports if structure analysis and 3D-NOESY assignment were successful.