The description of protein backbone was recently improved with a group of structural fragments called Structural
Alphabets instead of the regular three states (Helix, Sheet and Coil) secondary structure description. Protein Blocks
is one of the Structural Alphabets used to describe each and every region of protein backbone including the coil. According
to de Brevern (2000) the Protein Blocks has 16 structural fragments and each one has 5 residues in length. Protein
Blocks fragments are highly informative among the available Structural Alphabets and it has been used for many applications.
Here, we present a protein fold recognition method based on Protein Blocks for the annotation of twilight zone sequences.
In our method, we align the predicted Protein Blocks of a query amino acid sequence with a library of assigned
Protein Blocks of 953 known folds using the local pair-wise alignment. The alignment results with z-value ≥ 2.5 and Pvalue
≤ 0.08 are predicted as possible folds. Our method is able to recognize the possible folds for nearly 35.5% of the
twilight zone sequences with their predicted Protein Block sequence obtained by pb_prediction, which is available at Protein
Block Export server.
Keywords: Local protein structure, pairwise local alignment, protein block, protein folds recognition, secondary structure,
Structural alphabet, twilight zone sequences, computational method, three dimensional (3D) structure, alignment, technique
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