Effective parallelization of non-bonded interactions kernel for virtual screening on GPUs

Advances in Intelligent and Soft Computing

Volumn 93, Issue , 2011, Pages 63-69

  Guerrero, Ginés D ^a   Pérez Sánchez, Horacio ^b   Wenzel, Wolfgang ^b   Cecilia, José M ^a   García, José M ^a  

^a Grupo de Arquitectura y Computación Paralela   (Spain)

^b KARLSRUHE INSTITUTE OF TECHNOLOGY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

NONBONDED INTERACTION; PARALLELIZATIONS; VIRTUAL SCREENING;

PARALLEL ARCHITECTURES; PROGRAM PROCESSORS;

BIOINFORMATICS;

EID: 80052936701     PISSN: 18675662     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-3-642-19914-1_9     Document Type: Conference Paper

References (8)

1. Harvey, M.J., De Fabritiis, G.: An Implementation of the Smooth Particle Mesh Ewald Method on GPU Hardware. J. Chem. Theory. Comput. 5, 2371-2377 (2009)
2. Kokh, D., Wenzel, W.: Flexible side chain models improve enrichment rates in in silico screening. J. Med. Chem. 51, 5919-5931 (2008)
3. NVIDIA. CUDA Programming Guide 3.2 (2010)
4. Pérez-Sánchez, H.E.,Wenzel,W.: Implementation of an effective non-bonded interactions kernel for biomolecular simulations on the cell processor. In: Gesellschaft fuer Informatik, Jahrestagung 2009. LNI, vol. 154, pp. 721-729 (2009)
5. Pérez-Sánchez, H.E., Wenzel, W.: Optimization methods for virtual screening on novel computational architectures. Curr. Comput. Aided. Drug. Des. 7, 1-17 (2011)
6. Pham, D., Aipperspach, T., Boerstler, D., Bolliger, M., Chaudhry, R., Cox, D., Harvey, P., Hofstee, H., Johns, C.: Overview of the architecture, circuit design, and physical implementation of a first-generation cell processor. IEEE J. Solid-State Circuits 41, 179-196 (2006) (Pubitemid 43145976)
7. Schiller, A., Sutmann, G., Yang, L.: A Fast Wavelet Based Implementation to Calculate Coulomb Potentials on the Cell/B.E. In: Proceedings of the 2008 10th IEEE ICHPCC, pp. 162-168. IEEE Computer Society, Los Alamitos (2008)
8. Stone, J.E., Phillips, J.C., Freddolino, P.L., Hardy, D.J., Trabuco, L.G., Schulten, K.: Accelerating molecular modeling applications with graphics processors. J. Comput. Chem. 28, 2618-2640 (2007) (Pubitemid 350074136)