parallel conformational search of small molecules

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.

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.

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

Conformational Search: Sequencial Problem

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.

Parallel Computing, Solution?

Parallel Computing Model:

• Multiple Processors.

• The problem can be split distributing the data or the functionalities.

MIMD: Shared Memory MIMD:Distributed memory

Parallel Computing Models

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

Propoused Parallel Solution

•  Master – Worker Topology

Representación de Topología

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.

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.

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