General Data Compositional Data Distribution of Physicochemical characteristics

Physicochemical properties such as hydrophobicity, net charge, amphipathicity, interaction with bacterial cell envelope determine the mechanism of action of AMP. In turn, physicochemical properties are determined by amino acid sequences, for example, by amino acid compositions and distribution of particular amino acids along the chain. As different amino acid compositions and distribution dictate various mechanisms of action, knowing the difference between the sequences of distinct groups of AMPs is of utmost interest, for example, between linear and non-linear, long (> 25 AA) and short (< 15 AA), between AMPs active against different species. The current tool relying on DBAASP data allows performing such assessments for sequences consisting of standard amino acids. The parameter "Minimal Peptide count" means a threshold at which statistical measurements will not be performed. The user can choose a convenient value of the threshold. The default value equals 100.

Positively Charged Negatively Charged Hydrophobic Small Polar Uncharged Unusual
Amino acid composition of peptides from DBAASP relative to UniProt
Positively Charged Negatively Charged Hydrophobic Small Polar Uncharged Unusual

Distribution of i-spaced amino acid pairs (DiSAAP) is presented as the statistics of occurrence of amino acid pairs separated by i number of residues (i = 0,1,2,...,10) along the chain. For constructing a DiSAAP for particular amino acid or a specific group of amino acids, a special indicator "X" should be selected from the menu "Type of Task". Consequently, the row of menus for selection X will appear. X presents a particular amino acid (for example, A or G or R) or group of amino acids (for example, hydrophobic (L, I, V, F, A, W) or charged (R, K, E, D) or any desired group). For constructing a DiSAAP for two different groups of amino acids, the indicator "XY" will be picked from the menu "Type of Task". In this case, two rows of the menu will appear to select X and Y amino acids. X and Y present a particular amino acid (for example, A or G or R) or group of amino acids (for example, hydrophobic (L, I, V, F, A, W) or charged (R, K, E, D) or any desired group). X and Y should be different. Statistics built for XY pair differs from statistics for YX pair. The X should be picked from the upper row of menus and Y from the lower row. Statistics are presented with observed frequencies fi (based on the DBAASP data), an average value of expected frequencies Fi, and their standard deviation σi (i=0,1,2,...,10). Expected frequencies are estimated for random sequences generated by random shuffling of sequences of the considered set of peptides. Shuffling is repeated 500 times to assess average and standard deviation.


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Distribution of pair of residues of X () type separated by i residues (i=0,1,2,...,10).
Distribution of pair of residues of X () and Y () types separated by i residues (i=0,1,2,...,10).
Fi+ 3σi fi Fi- 3σi