General Data Compositional DataNEW Distribution of Physicochemical characteristicsNEW

Physicochemical features of AMP , such as hydrophobicity, charge, amphipathicity, predisposition to interaction with cell envelope and so on, determine the mode of action. Physicochemical features are determined by amino acid sequences, for example, by amino acid compositions and distribution of particular amino acids along the chain. Mode of action determined by amino acid compositions and distributions can be different. So, it's interesting to know differences in amino acid compositions and distributions along the chain between different groups of AMPs, for example: between linear and non-linear; between long ( > 25 aa) and short ( < 15 aa); between AMPs that are active against different species; etc . Current tool relying on DBAASP data allows to perform such assessments for sequences consisting of not modified amino acids. The parameter "Minimal Peptide count" means a threshold for which statistics will not be assessed. User can choose convenient value of threshold. The default value equals 100;









Positively Charged Negatively Charged Hydrophobic Small Polar Uncharged Unusual








Positively Charged Negatively Charged Hydrophobic Small Polar Uncharged Unusual

If a Pairwise distribution of particular amino acid or certain group of amino acids has to be constructed, special indicator "X" should be chosen in the menu " Type of Task". Consequently the raw of menus for selection X will appear. So, X will present a particular amino acid (for example A or G or R etc) or group of amino acids (for example hydrophobic (L,I,V,F,A,W) or charged (R, K, E, D) or any group desired). Pairwise distribution of X will be presented as a statistics of occurrence of pair of X type of amino acid separated along the chain by i residues ( i = 0,1,2,...,10).

If the indicator "XY" will be chosen in the menu " Type of Task", a Pairwise distribution of X and Y amino acids , or two different groups of amino acids will be constructed. In the case of indicator of "XY" two raw of menus for selection of X and Y will appear. X and Y present a particular amino acid (for example A or G or R etc) or group of amino acids (for example hydrophobic (L,I,V,F,A,W) or charged (R, K, E, D) or any group desired). X and Y should be different. In general, statistics built for XY pair is distinguished from statistics built for YX pair. The X should be chosen from upper raw of menus and Y from lower raw. Pairwise distribution will be presented as a statistics of occurrence of pair of X and Y type of amino acids separated along the chain by i residues ( i = 0,1,2,...,10)

Statistics has presented by observed frequencies fi ( relied on the DBAASP data), 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 considered set of peptides. Shuffling is repeated 500 times to assess average and standard deviation.










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Fi+ 3σi fi Fi- 3σi

Distribution of the values of Physicochemical characteristics for the sets of peptides from DBAASP

A desired characteristic has to be chosen at the menu "Physicochemical Characteristics", to build a distribution of the values of corresponding characteristic for the sets of peptides defined by different values of parameters: "sequence length", "synthesis type" , "target group" and "bond".