An approach to protein folding on the grid – EuChinaGRID experience

• Autorzy: Malawski M. , Szepieniec T. , Kochanczyk M. , Piwowar M. , Roterman I.
• Języki publikacji: EN

Abstrakty

EN

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.

Słowa kluczowe

EN

protein folding simulation; grid system; pharmacology; drug design

• Wydawca: Uniwersytet Jagielloński - Collegium Medicum ; Index Copernicus Sp. z o.o.
• Czasopismo: Bio-Algorithms and Med-Systems
• Rocznik: 2007
• Tom: Vol. 3, no. 5
• Strony: 45--49
• Opis fizyczny: Bibliogr. 18 poz., zdj.

Twórcy

autor

Malawski M.

• Institute of Computer Science, AGH, Al. Mickiewicza 30, 30-059 Kraków, Poland

autor

Szepieniec T.

• Academic Computer Center CYFRONET, ul. Nawojki 11, 30-950 Kraków, Poland

autor

Kochanczyk M.

• Department of Bioinformatics and Telemedicine, Jagiellonian University, Collegium Medicum, ul. Św. Anny 12, 31-008 Kraków, Poland

autor

Piwowar M.

• Department of Bioinformatics and Telemedicine, Jagiellonian University, Collegium Medicum, ul. Św. Anny 12, 31-008 Kraków, Poland

autor

Roterman I.

• Department of Bioinformatics and Telemedicine, Jagiellonian University, Collegium Medicum, ul. Św. Anny 12, 31-008 Kraków, Poland

Bibliografia

• 1. IST EUChinaGRID Project. Project website: http://www.euchinagrid.org.
• 2. Brylinski M., Konieczny L., Czerwonko P., Jurkowski W., Roterman I.: Earlystage folding in proteins (in silico) – sequence to structure relation, J Biomed Biotechnol, 2 (2005) 65-79.
• 3. Natrajan A., Crowley M., Wilkins-Diehr N., Humphrey M., Fox A., Grimshaw A., and Brooks III C.: Studying Protein Folding on the Grid: Experiences using CHARMM on NPACI Resources under Legion. Proceedings of the HPDC Conference (2001), San Francisco, USA.
• 4. Berkeley Open Infrastructure for Network Computing. Project website: http://boinc.berkeley.edu.
• 5. Taufer M., An C., and Kerstens A., Brooks III Ch. L.: Predictor@Home: A ’Protein Structure Prediction Supercomputer’ Based on Global Computing, IEEE Transactions on Parallel and Distributed Systems, 17, 8 (2006) 786-796.
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• 7. Rohl C.A., Strauss C.E., Misura K.M., Baker D.: Protein structure prediction using Rosetta, Methods Enzymol, 383 (2004) 66-93.
• 8. Human Proteome Folding Project. Project website: http://www.grid.org/projects/hpf.
• 9. Jurkowski W., Brylinski M., Wisniowski Z., Roterman I.: The conformational subspace in simulation of early-stage protein folding, Proteins, 55 (2004) 115-127.
• 10. Brylinski M., Jurkowski W., Konieczny L., Roterman I.: Limited conformational space for early-stage protein folding simulation, Bioinformatics, 20 (2004) 199-205.
• 11. Brylinski M., Konieczny L., Roterman I.: Fuzzy oil-drop hydrophobic force field – a model to represent late stage folding (in silico) of lysozyme, J Biomol Struct Dyn, 23 (2006) 519-528.
• 12. Brylinski M., Kochanczyk M., Konieczny L., Roterman I.: Sequence-structure-function relation characterized in silico, In Silico Biol, 6 (2006) 0052.
• 13. GridSphere Portal. Product website: http://www.gridsphere.org.
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• 18. Chiarabelli C., Vrijbloed J.W., De Lucrezia D., Thomas R.M., Stano P., Polticelli F., Ottone T., Papa E., Luisi P.L.: Investigation of de novo Totally Random Biosequences, Part II, Chemistry and Biodiversity, 3, 8 (2006) 840-859.