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The topology predictor SPLIT 4.0 (http://pref.etfos.hr) predicts the sequence location of transmembrane helices by performing an automatic selection of optimal amino acid attribute and corresponding preference functions. The best topological model is selected by choosing the highest absolute bias parameter that combines the bias in basic charge motifs and(More)
SUMMARY Anuran tissues, and especially skin, are a rich source of bioactive peptides and their precursors. We here present a manually curated database of antimicrobial and other defense peptides with a total of 2571 entries, most of them in the precursor form with demarcated signal peptide (SP), acidic proregion(s) and bioactive moiety(s) corresponding to(More)
We have created a structure-selectivity database (AMPad) of frog-derived, helical antimicrobial peptides (AMPs), in which the selectivity was determined as a therapeutic index (TI), and then used the novel concept of sequence moments to study the lengthwise asymmetry of physicochemical peptide properties. We found that the cosine of the angle between two(More)
In contrast to the standard derivation of Kirchhoff's loop law, which invokes electric potential, we show, for the linear planar electric network in a stationary state at the fixed temperature, that loop law can be derived from the maximum entropy production principle. This means that the currents in network branches are distributed in such a way as to(More)
Steady-state bacterial photosynthesis is modelled as cyclic chemical reaction and is examined with respect to overall efficiency, power transfer efficiency, and entropy production. A nonlinear flux-force relationship is assumed. The simplest two-state kinetic model bears complete analogy with the performance of an ideal (zero ohmic resistance of the P-N(More)
The preference functions method is described for prediction of membrane-buried helices in membrane proteins. Preference for the alpha-helix conformation of amino acid residue in a sequence is a non-linear function of average hydrophobicity of its sequence neighbors. Kyte-Doolittle hydropathy values are used to extract preference functions from a training(More)
Anuran skin is known to be a rich source of antimicrobial peptides although their therapeutic potential is often limited due to their toxicity against mammalian cells. The analysis of structure-activity relationships among anuran antimicrobial peptides provided the parameters to construct the "Mutator" tool for improving their selectivity for bacterial(More)
A method based on the use of signal peptide sequences from antimicrobial peptide (AMP) precursors was used to mine a placozoa expressed sequence tag database and identified a potential antimicrobial peptide from Trichoplax adhaerens. This peptide, with predicted sequence FFGRLKSVWSAVKHGWKAAKSR is the first AMP from a placozoan species, and was named(More)