Predicting three-dimensional structure of protein fragments from dihedral angle propensities and molecular dynamics.

Incorporating the existing knowledge of protein structural preferences, e.g., amino acid angle frequencies, in structure prediction have proven to be less successful with smaller peptides.

A computational approach for peptidomic analysis in taxonomic study of amphibian species.

Peptides in the skin secretion of frogs have been studied for some time now because they frequently possess important biological activity such as antibiotic, antimicrobial, or anticancer properties. In this paper, we present a computational approach for measuring the degree of similarity between the entire peptide complement of the skin secretion of specimens from the same or different species. The first step in the analysis is the generation of a mass spectral profile from an experimental high-performance liquid chromatography/electrosparay ionization analysis of the sample.

Heuristic charge assignment for deconvolution of electrospray ionization mass spectra.

We propose a new algorithm for deconvolution of electrospray ionization mass spectra based on direct assignment of charge to the measured signal at each mass-to-charge ratio (m/z). We investigate two heuristics for charge assignment: the entropy-based heuristic is adapted from a deconvolution algorithm by Reinhold and Reinhold;10 the multiplicative-correlation heuristic is adapted from the multiplicative-correlation deconvolution algorithm of Hagen and Monnig.6 The entropy-based heuristic is insensitive to overestimates of z(max), the maximum ion charge.