virtual screnning, docking, MPI

1. 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.

2. 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.

3. 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

4. Conformational Search: Sequencial Problem

5. 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.

7. Parallel Computing, Solution?
Parallel Computing Model:
• Multiple Processors.
• The problem can be split distributing the data or
the functionalities.

8. Parallel Computing Models
MIMD: Shared Memory MIMD:Distributed memory

9. Analysis and Design
Partición: Domain or Function.
Comunication.
Combine Tasks
Final Results
Foster, Ian. Desingning and Building Parallel Programs. http://wwwunix.
msc.anl.gov/dbpp/text/book, 2003.

10. Propoused Parallel Solution
• Master – Worker Topology
Representación de Topología

11. 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.

13. Results
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
Algorithm results for molecules of 5 rotables bonds
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.

14. 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