Publications(2011)

  1. Community-wide assessment of protein-interface modeling suggests improvements to design methodology.
    Fleishman SJ, Whitehead TA, Strauch EM, Corn JE, Qin S, Zhou HX, Mitchell JC, Demerdash ON, Takeda-Shitaka M, Terashi G, Moal IH, Li X, Bates PA, Zacharias M, Park H, Ko JS, Lee H, Seok C, Bourquard T, Bernauer J, Poupon A, Azé J, Soner S, Ovalı SK, Ozbek P, Tal NB, Haliloglu T, Hwang H, Vreven T, Pierce BG, Weng Z, Pérez-Cano L, Pons C, Fernández-Recio J, Jiang F, Yang F, Gong X, Cao L, Xu X, Liu B, Wang P, Li C, Wang C, Robert CH, Guharoy M, Liu S, Huang Y, Li L, Guo D, Chen Y, Xiao Y, London N, Itzhaki Z, Schueler-Furman O, Inbar Y, Potapov V, Cohen M, Schreiber G, Tsuchiya Y, Kanamori E, Standley DM, Nakamura H, Kinoshita K, Driggers CM, Hall RG, Morgan JL, Hsu VL, Zhan J, Yang Y, Zhou Y, Kastritis PL, Bonvin AM, Zhang W, Camacho CJ, Kilambi KP, Sircar A, Gray JJ, Ohue M, Uchikoga N, Matsuzaki Y, Ishida T, Akiyama Y, Khashan R, Bush S, Fouches D, Tropsha A, Esquivel-Rodríguez J, Kihara D, Stranges PB, Jacak R, Kuhlman B, Huang SY, Zou X, Wodak SJ, Janin J, Baker D.
    J Mol Biol. 2011 Nov 25;414(2):289-302. Epub 2011 Sep 29.
    PMID: 22001016 [PubMed – in process]
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  2. Assessing the utility of gene co-expression stability in combination with correlation in the analysis of protein-protein interaction networks
    A Patil, K Nakai, K Kinoshita.
    BMC Genomics. 2011 Nov 30;12 Suppl 3:S19. Epub 2011 Nov 30.
    PMID: 22369639 [PubMed – in process]
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  3. Absolute quality evaluation of protein model structures using statistical potentials with respect to the native and reference states.
    Shirota M, Ishida K, Kasahara K, Kinoshita K.
    Proteins. 2011 May;79(5):1550-63. doi: 10.1002/prot.22982. Epub 2011 Mar 1.
    PMID: 21365682 [PubMed – indexed for MEDLINE]
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  4. ATTED-II updates: condition-specific gene coexpression to extend coexpression analyses and applications to a broad range of flowering plants.
    Obayashi T, Nishida K, Kasahara K, Kinoshita K.
    Plant Cell Physiol. 2011 Feb;52(2):213-9. Epub 2011 Jan 7.
    PMID: 21217125 [PubMed – indexed for MEDLINE]
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  5. COXPRESdb: a database to compare gene coexpression in seven model animals.
    Obayashi T, Kinoshita K.
    Nucleic Acids Res. 2011 Jan;39(Database issue):D1016-22. Epub 2010 Nov 16.
    PMID: 21081562 [PubMed – indexed for MEDLINE]
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  6. SAHG, a comprehensive database of predicted structures of all human proteins.
    Motono C, Nakata J, Koike R, Shimizu K, Shirota M, Amemiya T, Tomii K, Nagano N, Sakaya N, Misoo K, Sato M, Kidera A, Hiroaki H, Shirai T, Kinoshita K, Noguchi T, Ota M
    Nuclieic Acids Res. 2011 Jan;39(Database issue):D487-93 , Epub 2010 Nov 3.
    PMID: 21051360 [PubMed – indexed for MEDLINE]
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