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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)
A suite of FORTRAN programs, PREF, is described for calculating preference functions from the data base of known protein structures and for comparing smoothed profiles of sequence-dependent preferences in proteins of unknown structure. Amino acid preferences for a secondary structure are considered as functions of a sequence environment. Sequence(More)
Several authors have proposed that predictions of protein secondary structure derived from statistical information about the known structures can be improved when information about neighboring residues participating in short and medium range interactions is included. A substantial improvement shown here indicates that current methods of including this(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)
A challenge when designing membrane-active peptide antibiotics with therapeutic potential is how to ensure a useful antibacterial activity whilst avoiding unacceptable cytotoxicity for host cells. Understanding their mode of interaction with membranes and the reasons underlying their ability to distinguish between bacterial and eukaryotic cytoplasmic cells(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)
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)
The problem of multidrug resistance requires the efficient and accurate identification of new classes of antimicrobial agents. Endogenous antimicrobial peptides produced by most organisms are a promising source of such molecules. We have exploited the high conservation of signal sequences in teleost and anuran antimicrobial peptides to search cDNA(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)