Calculation of Force Field Grids for Molecular Docking Using Graphics Processing Unit
The vast majority of problems faced by bioinformatics are very complex and time consuming. They require the use of modern high-performance computational systems and the development of algorithms for such system. Heterogeneous computing systems which include graphics processing unit (GPU) occupy a se...
| Main Author: | |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Siberian Federal University
2014-03-01
|
| Series: | Журнал Сибирского федерального университета: Серия Биология |
| Subjects: | |
| Online Access: | http://elib.sfu-kras.ru/bitstream/2311/13339/4/01_Farkov_2.pdf |
| _version_ | 1818849234402672640 |
|---|---|
| author | Mikhail A. Farkov |
| author_facet | Mikhail A. Farkov |
| author_sort | Mikhail A. Farkov |
| collection | DOAJ |
| description | The vast majority of problems faced by bioinformatics are very complex and time consuming. They require the use of modern high-performance computational systems and the development of algorithms for such system. Heterogeneous computing systems which include graphics processing unit (GPU) occupy a separate niche. Such systems allow to accelerate solving of some task significantly. The task performing molecular docking namely accelerating the calculation of force field grids for fast ligandprotein molecular docking is studied in this work. Algorithms for fast calculation of the large number of force field grids which are scaled to all GPUs available in the system were developed. Extensive testing on different platforms was performed |
| first_indexed | 2024-12-19T06:30:00Z |
| format | Article |
| id | doaj.art-6908409584ff4945b128a1328b19c477 |
| institution | Directory Open Access Journal |
| issn | 1997-1389 2313-5530 |
| language | English |
| last_indexed | 2024-12-19T06:30:00Z |
| publishDate | 2014-03-01 |
| publisher | Siberian Federal University |
| record_format | Article |
| series | Журнал Сибирского федерального университета: Серия Биология |
| spelling | doaj.art-6908409584ff4945b128a1328b19c4772022-12-21T20:32:25ZengSiberian Federal UniversityЖурнал Сибирского федерального университета: Серия Биология1997-13892313-55302014-03-0171413http://elib.sfu-kras.ru/handle/2311/13339Calculation of Force Field Grids for Molecular Docking Using Graphics Processing UnitMikhail A. Farkov0Siberian Federal University 79 Svobodny, Krasnoyarsk, 660041, RussiaThe vast majority of problems faced by bioinformatics are very complex and time consuming. They require the use of modern high-performance computational systems and the development of algorithms for such system. Heterogeneous computing systems which include graphics processing unit (GPU) occupy a separate niche. Such systems allow to accelerate solving of some task significantly. The task performing molecular docking namely accelerating the calculation of force field grids for fast ligandprotein molecular docking is studied in this work. Algorithms for fast calculation of the large number of force field grids which are scaled to all GPUs available in the system were developed. Extensive testing on different platforms was performedhttp://elib.sfu-kras.ru/bitstream/2311/13339/4/01_Farkov_2.pdfGPGPUCUDAmolecular dockingvirtual screeningligand-protein dockingGPGPUCUDA |
| spellingShingle | Mikhail A. Farkov Calculation of Force Field Grids for Molecular Docking Using Graphics Processing Unit Журнал Сибирского федерального университета: Серия Биология GPGPU CUDA molecular docking virtual screening ligand-protein docking GPGPU CUDA |
| title | Calculation of Force Field Grids for Molecular Docking Using Graphics Processing Unit |
| title_full | Calculation of Force Field Grids for Molecular Docking Using Graphics Processing Unit |
| title_fullStr | Calculation of Force Field Grids for Molecular Docking Using Graphics Processing Unit |
| title_full_unstemmed | Calculation of Force Field Grids for Molecular Docking Using Graphics Processing Unit |
| title_short | Calculation of Force Field Grids for Molecular Docking Using Graphics Processing Unit |
| title_sort | calculation of force field grids for molecular docking using graphics processing unit |
| topic | GPGPU CUDA molecular docking virtual screening ligand-protein docking GPGPU CUDA |
| url | http://elib.sfu-kras.ru/bitstream/2311/13339/4/01_Farkov_2.pdf |
| work_keys_str_mv | AT mikhailafarkov calculationofforcefieldgridsformoleculardockingusinggraphicsprocessingunit |