메뉴 건너뛰기




Volumn , Issue , 2009, Pages 380-389

Single-particle 3D reconstruction from cryo-electron microscopy images on GPU

Author keywords

Cryo EM; GPU; Many core; Performance tuning

Indexed keywords

3D RECONSTRUCTION; 3D STRUCTURE; BIOLOGICAL MOLECULE; COMPUTATIONAL INTENSITY; COMPUTATIONAL REQUIREMENTS; CRYO-ELECTRON MICROSCOPY; DATA MAPPINGS; DECOUPLE COMPUTATION; FLOATING POINT UNITS; HIGH RESOLUTION; KERNEL APPLICATIONS; MANY-CORE; MEMORY BANDWIDTHS; MEMORY OPERATIONS; MEMORY PERFORMANCE; MULTICORE ARCHITECTURES; OFF-CHIP MEMORIES; OPEN-SOURCE; OPTIMIZATION STRATEGY; SINGLE-PARTICLE;

EID: 70449732743     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1145/1542275.1542329     Document Type: Conference Paper
Times cited : (17)

References (22)
  • 1
    • 33750023228 scopus 로고    scopus 로고
    • A microbenchmark suite for openmp 2.0
    • J. Bull and D. O'Neill. A microbenchmark suite for openmp 2.0. SIGARCH Comput. Archit. News, 29(5):41-48, 2001.
    • (2001) SIGARCH Comput. Archit. News , vol.29 , Issue.5 , pp. 41-48
    • Bull, J.1    O'Neill, D.2
  • 3
    • 0000668797 scopus 로고
    • A reconstruction of 3-dimensional structure from electron micrographs
    • D. DeRosier and A. Klug. A reconstruction of 3-dimensional structure from electron micrographs. Nature, 217:130-134, 1968.
    • (1968) Nature , vol.217 , pp. 130-134
    • DeRosier, D.1    Klug, A.2
  • 4
    • 33845286204 scopus 로고    scopus 로고
    • Implementation and performance evaluation of reconstruction algorithms on graphics processors
    • D. Diez, H. Mueller, and A. Frangakis. Implementation and performance evaluation of reconstruction algorithms on graphics processors. Journal of Structural Biology, 157:288-295, 2007.
    • (2007) Journal of Structural Biology , vol.157 , pp. 288-295
    • Diez, D.1    Mueller, H.2    Frangakis, A.3
  • 6
    • 70449732294 scopus 로고    scopus 로고
    • FFTW
    • FFTW. www.fftw.org.
  • 7
    • 70449715280 scopus 로고    scopus 로고
    • GPU Technology for Accelerated Computing
    • GPU Technology for Accelerated Computing. www.amd.com/stream.
  • 8
    • 0029975088 scopus 로고    scopus 로고
    • J. Frank, Radermacher, Penczek M., P. Zhu, J., Y. Li, and Ladjadj. Spider and web: processing and visualization of images in 3d electron microscopy and related fields. Journal of Structural Biology, 116:190-199, 1996.
    • J. Frank, Radermacher, Penczek M., P. Zhu, J., Y. Li, and Ladjadj. Spider and web: processing and visualization of images in 3d electron microscopy and related fields. Journal of Structural Biology, 116:190-199, 1996.
  • 10
    • 70449701606 scopus 로고    scopus 로고
    • GPGPU
    • GPGPU. http://www.gpgpu.org.
  • 14
    • 0036420061 scopus 로고    scopus 로고
    • Imirs: A high-resolution 3d reconstruction package integrated with a relational image database
    • Y. Liang, E. Y. Ke, and Z. H. Zhou. Imirs: a high-resolution 3d reconstruction package integrated with a relational image database. Journal of Structural Biology, 137:292-304, 2002.
    • (2002) Journal of Structural Biology , vol.137 , pp. 292-304
    • Liang, Y.1    Ke, E.Y.2    Zhou, Z.H.3
  • 15
    • 0033377664 scopus 로고    scopus 로고
    • Eman: Semiautomated software for high-resolution single-particle reconstructions
    • S. Ludtke, P. Baldwin, and W. Chiu. Eman: Semiautomated software for high-resolution single-particle reconstructions. Journal of Structural Biology, 128(1):82-97, 1999.
    • (1999) Journal of Structural Biology , vol.128 , Issue.1 , pp. 82-97
    • Ludtke, S.1    Baldwin, P.2    Chiu, W.3
  • 17
    • 33845939047 scopus 로고    scopus 로고
    • Disentangling conformational states of macromolecules in 3d-em through likelihood optimization
    • S.H. Scheres, M. Valle H. Gao, G.T.Herman, P.P. Eggermont, J. Frank, and J.M.Carazo. Disentangling conformational states of macromolecules in 3d-em through likelihood optimization. Nature, 4(1):27-29, 2007.
    • (2007) Nature , vol.4 , Issue.1 , pp. 27-29
    • Scheres, S.H.1    Valle, M.2    Gao, H.3    Herman, G.T.4    Eggermont, P.P.5    Frank, J.6    Carazo, J.M.7
  • 19
    • 0016391518 scopus 로고
    • Electron diffraction of frozen, hydrated protein crystals
    • K. Taylor and R. M. Glaeser. Electron diffraction of frozen, hydrated protein crystals. Science, 186:1036-1037, 1974.
    • (1974) Science , vol.186 , pp. 1036-1037
    • Taylor, K.1    Glaeser, R.M.2
  • 21
    • 23444434540 scopus 로고    scopus 로고
    • A hybrid condensed finite element model with gpu acceleration for interactive 3d soft tissue cutting: Research articles
    • W. Wu and P. Heng. A hybrid condensed finite element model with gpu acceleration for interactive 3d soft tissue cutting: Research articles. Computer Animation and Virtual Worlds, 15(3):219-227, 2004.
    • (2004) Computer Animation and Virtual Worlds , vol.15 , Issue.3 , pp. 219-227
    • Wu, W.1    Heng, P.2
  • 22
    • 51049115771 scopus 로고    scopus 로고
    • A parallel software toolkit for statistical 3-d virus reconstructions from cryo electron microscopy images using computer clusters with multi-core shared-memory nodes
    • Y. Zheng and P. C. Doerschuk. A parallel software toolkit for statistical 3-d virus reconstructions from cryo electron microscopy images using computer clusters with multi-core shared-memory nodes. In 22rd IEEE International Parallel and Distributed Processing Symposium, 2008.
    • (2008) 22rd IEEE International Parallel and Distributed Processing Symposium
    • Zheng, Y.1    Doerschuk, P.C.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.