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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.