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Drug-Target Interactionͽ¬ †
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BO-DTI †
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- Tomohiro Ban, Masahito Ohue, Yutaka Akiyama: "Efficient Hyperparameter Optimization by Using Bayesian Optimization for Drug-Target Interaction Prediction", In Proceedings of the 7th IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS 2017), Orlando, FL, USA, October 19-21, 2017. (accepted)
[ Paper | Slide ]
http://www.github.com/akiyamalab/BO-DTI
Link Indicator Kernel †
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- Masahito Ohue, Takuro Yamazaki, Tomohiro Ban, Yutaka Akiyama: "Link Mining for Kernel-based Compound-Protein Interaction Predictions Using a Chemogenomics Approach", In Proceedings of the Thirteenth International Conference On Intelligent Computing (ICIC2017) (Lecture Notes in Computer Science), 10362, 549-558, Liverpool,UK August 7-10, 2017.
[ Paper | arXiv | Slide ]
Spresso †
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http://www.bi.cs.titech.ac.jp/spresso
- Keisuke Yanagisawa, Shunta Komine, Shogo D. Suzuki, Masahito Ohue, Takashi Ishida, Yutaka Akiyama: "Spresso: An ultrafast compound pre-screening method based on compound decomposition", Bioinformatics. (in press)
[ PubMed | Journal Website ]
- Keisuke Yanagisawa, Shunta Komine, Shogo D. Suzuki, Masahito Ohue, Takashi Ishida, Yutaka Akiyama: "ESPRESSO: An ultrafast compound pre-screening method based on compound decomposition", In Proceedings of The 27th International Conference on Genome Informatics (GIW 2016), 2016.
MEGADOCK †
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NVIDIA Application Catalog¤Ë¤â·ÇºÜ¤µ¤ì¤Æ¤¤¤Þ¤¹¡§https://www.nvidia.com/en-us/data-center/gpu-accelerated-applications/catalog/
¥¿¥ó¥Ñ¥¯¼Á´Ö¥É¥Ã¥¥ó¥°Í½Â¬ †
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- Masahito Ohue†, Yuri Matsuzaki†, Nobuyuki Uchikoga, Takashi Ishida, Yutaka Akiyama: "MEGADOCK: An all-to-all protein-protein interaction prediction system using tertiary structure data", Protein and Peptide Letters, 21(8): 766-778, 2014.
[ PubMed | BenthamScience ]
¿·¤·¤¤¥Ü¥¯¥»¥ë¥¹¥³¥¢¥â¥Ç¥ë¤Î³«È¯ †
rPSC¤È¸Æ¤Ð¤ì¤ëÆȼ«¤Î·Á¾õÁêÊäÀ¥¹¥³¥¢¥â¥Ç¥ë¤ò¥Ù¡¼¥¹¤È¤·¡¤ÀÅÅÅÁê¸ßºîÍѤäæ¿åϼ«Í³¥¨¥Í¥ë¥®¡¼¤ò¥â¥Ç¥ë²½¤·¤¿¡¤¹â®¤Ë·×»»²Äǽ¤Ê¥¹¥³¥¢¥â¥Ç¥ë¤òÄó°Æ¤·¤Æ¤¤¤Þ¤¹¡¥
- Masahito Ohue, Yuri Matsuzaki, Takashi Ishida, Yutaka Akiyama: "Improvement of the Protein-Protein Docking Prediction by Introducing a Simple Hydrophobic Interaction Model: an Application to Interaction Pathway Analysis", In Proceedings of The 7th IAPR International Conference on Pattern Recognition in Bioinformatics (PRIB2012), Lecture Notes in Bioinformatics 7632, 178-187, Springer Heidelberg, 2012.
[ SpringerLink | Slide | Streaming(e-Bio) ]
High Performance Computing (HPC) †
ÊÂÎó·×»»µ¡¡Ê¥¹¡¼¥Ñ¡¼¥³¥ó¥Ô¥å¡¼¥¿¡Ë¤òÍøÍѤ·¤¿¥¿¥ó¥Ñ¥¯¼Á¥É¥Ã¥¥ó¥°Í½Â¬·×»»¤ò¹Ô¤¦¥½¥Õ¥È¥¦¥§¥¢¤ò³«È¯¤·¤Æ¤¤¤Þ¤¹¡¥
- Masahito Ohue†, Takehiro Shimoda†, Shuji Suzuki, Yuri Matsuzaki, Takashi Ishida, Yutaka Akiyama: "MEGADOCK 4.0: an ultra–high-performance protein–protein docking software for heterogeneous supercomputers", Bioinformatics, 30(22): 3281-3283, 2014.
[ PubMed | Oxford ]
- Yuri Matsuzaki, Nobuyuki Uchikoga, Masahito Ohue, Takehiro Shimoda, Toshiyuki Sato, Takashi Ishida, Yutaka Akiyama: "MEGADOCK 3.0: A high-performance protein-protein interaction prediction software using hybrid parallel computing for petascale supercomputing environments", Source Code for Biology and Medicine, 8(1): 18, 2013.
[ PubMed | BioMedCentral ]
¥¿¥ó¥Ñ¥¯¼Á´ÖÁê¸ßºîÍѥͥåȥ¥¯Í½Â¬ †
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- Masahito Ohue†, Yuri Matsuzaki†, Nobuyuki Uchikoga, Takashi Ishida, Yutaka Akiyama: "MEGADOCK: An all-to-all protein-protein interaction prediction system using tertiary structure data", Protein and Peptide Letters, 21(8): 766-778, 2014.
[ PubMed | BenthamScience ]
- Âç¾å²í»Ë, ¾¾ºêͳÍý, ¾¾ùõ͵²ð, º´Æ£ÃÒÇ·, ½©»³ÂÙ: ¡ÈMEGADOCK¡§Î©Âι½Â¤¾ðÊ󤫤é¤ÎÌÖÍåŪ¥¿¥ó¥Ñ¥¯¼Á´ÖÁê¸ßºîÍÑͽ¬¤È¤½¤Î¥·¥¹¥Æ¥àÀ¸Êª³Ø¤Ø¤Î±þÍÑ¡É, ¾ðÊó½èÍý³Ø²ñÏÀʸ»ï ¿ôÍý¥â¥Ç¥ë²½¤È±þÍÑ, 3(3): 91-106, 2010.
[ IPSJ Digital Library ]
¥¿¥ó¥Ñ¥¯¼Á-RNA´ÖÁê¸ßºîÍÑͽ¬ †
¥Ò¥È¥²¥Î¥àÃæ¤Ë¤Ïnon-coding RNA¤¬Ìó1500¸Ä¤Û¤É¥³¡¼¥É¤µ¤ì¤Æ¤¤¤ë¤È¤¤¤ï¤ì¤Æ¤ª¤ê¡¤¥¿¥ó¥Ñ¥¯¼ÁƱ»Î¤À¤±¤Ç¤Ê¤¯¡¤Â¿¿ô¤ÎRNA¤¬¥¿¥ó¥Ñ¥¯¼Á¤ÈÁê¸ßºîÍѤ·¤Æ¤¤¤Þ¤¹¡¥²æ¡¹¤ÏÆȼ«¤Î¥¿¥ó¥Ñ¥¯¼Á´ÖÁê¸ßºîÍÑͽ¬¤Î¼êË¡¤ò±þÍѤ·¤¿¡¤¿·¤·¤¤¥¿¥ó¥Ñ¥¯¼Á-RNA´ÖÁê¸ßºîÍÑͽ¬¤Î¼êË¡¤ò¸¦µæ¤·¤Æ¤¤¤Þ¤¹¡¥
- Masahito Ohue, Yuri Matsuzaki, Yutaka Akiyama: "Docking-calculation-based Method for Predicting Protein-RNA Interactions",
Genome Informatics, 25(1): 25-39, Aug 3 2011.
[ PubMed | J-stage ]
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- Yuri Matsuzaki†, Masahito Ohue†, Nobuyuki Uchikoga, Yutaka Akiyama: "Protein-protein interaction network prediction by using rigid-body docking tools: application to bacterial chemotaxis", Protein and Peptide Letters, 21(8): 790-798, 2014.
[ PubMed | BenthamScience ]
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¤³¤Î¸¦µæ¤Ç¤Ï¡¤MEGADOCK¤Ë¤è¤Ã¤Æ¥¢¥Ý¥È¡¼¥·¥¹¤Ë´ØÏ¢¤¹¤ë¥¿¥ó¥Ñ¥¯¼Á¤ÎÁê¸ßºîÍѥͥåȥ¥¯¤òͽ¬¤¹¤ë¤È¤È¤â¤Ë¡¤´ûÃÎÊ£¹çÂι½Â¤¤ò¥Æ¥ó¥×¥ì¡¼¥È¾ðÊó¤È¤·¤ÆÍøÍѤ¹¤ë¼êË¡¤ÈÁȤ߹ç¤ï¤»¤ë¤³¤È¤ÇŬ¹çΨ¤Î¹â¤¤Í½Â¬¤¬¹Ô¤¨¤ë¤³¤È¤ò¼¨¤·¤Þ¤·¤¿¡¥
- Masahito Ohue, Yuri Matsuzaki, Takehiro Shimoda, Takashi Ishida, Yutaka Akiyama: "Highly Precise Protein-Protein Interaction Prediction Based on Consensus Between Template-Based and de Novo Docking Methods", BMC Proceedings, 7(Suppl 7): S6, 2013.
[ PubMed | BioMedCentral ]