Parallel conformational search of small molecules
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Transcript of Parallel conformational search of small molecules
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Parallel conformational Search in small molecules
• Conformational search of small molecules.
• Sequencial Problem.
• Parallel Computation in MPI: Solution?
• Design and analysis of Parallel Applications.
• MPI implementation of Conformational Search of small molecules.
• Evaluation and results of the algorithm.
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Screening Virtual
Virtual screening has been defined as the "automatically evaluating very large libraries of compounds" using computer programs. VS has largely been a numbers game focusing on how the enormous chemical space of over 1060 conceivable compounds can be filtered to a manageable number that can be synthesized, purchased, and tested.
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Caso de Estudio: Búsqueda Conformacional sobre moléculas pequeñas.
Identificar las posibles conformaciones que puede adoptar el ligando en el sitio activo de la Proteína es uno de los pasos más importantes y complejos dentro de la primera etapa a la que se ha hecho referencia
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Conformational Search: Sequencial Problem
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Distribution of bond per molecules in Zinc Databases
Rotable Bonds Time of Sequential
Solution 5 247
10 3854
One file with 1000 molecules: 19 Hs.
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Parallel Computing, Solution?
Parallel Computing Model:
• Multiple Processors.
• The problem can be split distributing the data or the functionalities.
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MIMD: Shared Memory MIMD:Distributed memory
Parallel Computing Models
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Analysis and Design
Foster, Ian. Desingning and Building Parallel Programs. http://wwwunix. msc.anl.gov/dbpp/text/book, 2003.
Partición: Domain or Function. Comunication. Combine Tasks Final Results
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Propoused Parallel Solution
• Master – Worker Topology
Representación de Topología
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How to design thinking on performance
P0:processunit P1:processunit P2:processunit
Read Mols.
Send Comb. Submaster
Mol.
Recv Comb. Submaster
Mol.
Recv Comb. Submaster
Mol.
Search Conf. Search Conf.
Recv Conf. Send Conf.
Write Conf.
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Results
Algorithm results for molecules of 5 rotables bonds
No. Procesos TS(s) TP(s) Speed-up Eficiencia Isoeficiencia
4 105 57 1.842 46.05 1.17
6 105 38 2.763 46.05 1.17
8 105 27 3.889 48.61 1.06
10 105 27 3.889 38.89 1.57
No. Procesos TS(s) TP(s) Speed-up Eficiencia Isoeficiencia
4 1944 990 1.964 49.09 1.04 6 1944 520 3.738 62.31 0.60 8 1944 471 4.127 51.59 0.94 10 1944 276 7.043 70.43 0.42
Algorithm results for molecules of 10 rotable bonds.
No. Procesos TS(s) TP(s) Speed-up Eficiencia Isoeficiencia
4 39925 16961 2.354 58.85 0.70 6 39925 9252 4.315 71.92 0.39 8 39925 6528 6.116 76.45 0.31 10 39925 5083 7.855 78.55 0.27
Algorithm results for molecules of 15 rotable bonds.
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References
1. A UML-based Approach to Design Parallel and Distributed Applications. Y Perez-Riverol, RV Alvarez. arXiv preprint arXiv:1311.7011
2. A Parallel Systematic-Monte Carlo Algorithm for Exploring Conformational Space. Y Perez-Riverol, R Vera, Y Mazola, A Musacchio. Current Topics in Medicinal Chemistry 12 (16), 1790-1796