Learning biophysically-motivated parameters for alpha helix prediction

<p>Abstract</p> <p>Background</p> <p>Our goal is to develop a state-of-the-art protein secondary structure predictor, with an intuitive and biophysically-motivated energy model. We treat structure prediction as an optimization problem, using parameterizable cost functions representing biological "pseudo-energies". Machine learning methods are applied to estimate the values of the parameters to correctly predict known protein structures.</p> <p>Results</p> <p>Focusing on the prediction of alpha helices in proteins, we show that a model with 302 parameters can achieve a Q_{<it>α </it>}value of 77.6% and an SOV_{<it>α </it>}value of 73.4%. Such performance numbers are among the best for techniques that do not rely on external databases (such as multiple sequence alignments). Further, it is easier to extract biological significance from a model with so few parameters.</p> <p>Conclusion</p> <p>The method presented shows promise for the prediction of protein secondary structure. Biophysically-motivated elementary free-energies can be learned using SVM techniques to construct an energy cost function whose predictive performance rivals state-of-the-art. This method is general and can be extended beyond the all-alpha case described here.</p

Evadne anonyx G. O. Sars, 1897 – the first record of this Ponto-Caspian cladoceran in the Gulf of Gdańsk (Baltic Sea)* This research was conducted within the framework of project No. 4739/B/P01/2010/39 from the Polish National Sciences Centre.

Evadne anonyx, a new invasive Ponto-Caspian species, was detected for the first time in the Gulf of Gdańsk in the summer of 2006. Seven years probably elapsed from the first record of E. anonyx in the Baltic Sea (Gulf of Finland) to the first one in the Gulf of Gdańsk. Although the species was found at 10 out of 13 stations in rather low densities (not exceeding 6 indiv. m−3), all the developmental stages of E. anonyx were present (juveniles as well as adults – parthenogenetic females, gamogenetic females and males) in the plankton material investigated