Development of a method for Protein Remote Homologue
Detection Using Secondary Structure Prediction and
Solvent Accessibility Prediction.
Katsunori Uehara (0251137)
When we compare protein pairs, there are many protein pairs that share
the similar fold but have no clear sequence similarity (remote homologues).
To detect these remote homologues, we propose a new simple method
which combines the standard sequence search method with secondary
structure and solvent accessibility predictions. First sequence search
method is performed normally to get the sequence similarity (E-value)
between query and template sequences, next, secondary structure and
solvent accessibility are predicted for both query and template aligned
sequences by sequence search method. And then, Structure similarity
between predicted query and template structures are evaluated using
Zsocre. Final decision on whether they are remote homologous is made by
the combined score considering both E-value of the standard sequence
search method and the structure similarity. We used test using SCOP
database as the correct standard to check this method’s performance. This
study showed that the combination of E-value of sequence search method,
secondary structure and/or solvent accessibility predictions improved
BLAST/PSI-BLAST for detecting remote homologues.
Keywords:
Protein、Homologue、sequence homology、secondary structure、solvent
accessibility