Structural Biochemistry, Bioinformatics, Structural Alignments, Programs Used For Structural Alignment, DALI

DALI

DALI stands for Distance Alignment Matrix Method. DALI is a common and popular method that breaks down the protein that is inputted into hexapeptide fragments and then calculates a distance matrix through the understanding of the contact pattern between successive fragments. Secondary structure features with residues that are contiguous in sequence are shown on the matrix's main diagonal. The other diagonals represent residues that are not next to each other in sequence. When the diagonals are parallel to the main diagonal, the features they represent are also parallel. When the diagonals are perpendicular, however, their features are anti parallel.
If two proteins' distance matrices are the same or share similar features in almost the same positions, they can be said to have similar folds and length loops connecting the secondary structure elements. When two matrices are built, DALI's actual alignment process involves conducting a series of overlapping sub matrices that are 6x6. These 6x6 matrices are then reassembled to a final alignment through a standard score-maximization algorithm.
The DALI method has been used to construct the FSSP database (Fold classification based on structure-structure alignments of proteins, or families of structurally similar proteins). This database holds all known protein structures and aligns them with each other to determine structural neighbors and fold classification. This database information can easily be found on the internet for ease of access. A DALI online database can found here. A downloadable program and web search are other available DALI resources.

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