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An approach to protein folding on the grid – EuChinaGRID experience

Malawski M., Szepieniec T., Kochanczyk M., Piwowar M., Roterman I.

Bio-Algorithms and Med-Systems

2007

Vol. 3, no. 5

45--49

Contemporary pharmacology in its quest for more relevant and effective drugs needs to examine large range of biological structures to identify biological active compounds. We consider large grid environment the only platform to face such a computational challenge. In our project, the search is focused on peptide-like molecules containing about 70 amino acids in a single polypeptide chain. The limited number of proteins existing in the nature will be extended to those, which have not been recognized in any organisms (“never born proteins”). The assumption is that those which do not exist in the nature may also render biological activity, which directed on pharmacological use may correct some pathological phenomena. As the function results from the structure, two approaches are applied to predict cartesian coordinates of proteins’ atoms: sophisticated Monte Carlo structure creation, elimination and refinement using the Rosetta program and our own program for simulation of the protein folding process. As a computing platform we use the EuChinaGRID project resources, which are currently a part of EGEE infrastructure and are expanding to include Chinese resources as well. We describe the approach for porting the application to the grid and the prototype portal developed for simulation management and results analysis.

Nestbox grids in population studies of theCommon dormouse (Muscardinus avellanarius L.): methodological aspects

Juskaitis Rimvydas

Polish Journal of Ecology

2006

Vol. 54, nr 3

351-358

Two different nestbox grids have been used for studies of the common dormouse (Muscardinus avellanarius L.) populations: high-density nestbox grids in small plots (e.g. 25-30 boxes ha^-1 in 1 ha plots) and low-density nestbox grids in large plots (e.g. 4 boxes ha^-1 in areas of 60 and 85 ha). The present study aimed to compare efficiency and suitability of 25 x 25 m and 50 x 50 m nestbox grids for studies of the common dormouse population, and to show limitations of small study plots in dormouse studies. Live trapping of dormice within nestbox grids proved that all dormice captured used nestboxes placed in both 25 x 25 m and 50 x 50 m grids. Regular control of nestboxes placed in the 25 x 25 m grid gave an opportunity to register all adult dormice living in the study site during shorter periods, and average dormouse capture rate was significantly higher compared to the 50 x 50 m grid. However the 25 x 25 m nestbox grid had one substantial drawback: high nestbox density (16 boxes ha^-1) increased environment carrying capacity for dormice in the forest, where natural hollows were almost absent. In consequence, adult dormouse density increased two to four-fold, while their home range sizes decreased by about half. Dormice are distributed irregularly in large forest areas, and the results obtained in small study plots may not reflect the average characteristics of the population. Some results obtained in small study plots (e.g. density, mortality) can be overestimated because of dormouse movements and edge effects. Predators, e.g. owls, can catch some dormice and substantially influence the results obtained in small plots. Because of the influence on dormouse population density and other population parameters, high density nestbox grids (e.g. 20 x 20 m, 25 x 25 m) should not be used in dormouse population studies. Small study plots (e.g. 1 ha) are completely unsuitable for estimation of such dormouse population characteristics as survival (mortality) and dispersal.