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Items: 1 to 20 of 118

1.

KNApSAcK-3D: a three-dimensional structure database of plant metabolites.

Nakamura K, Shimura N, Otabe Y, Hirai-Morita A, Nakamura Y, Ono N, Ul-Amin MA, Kanaya S.

Plant Cell Physiol. 2013 Feb;54(2):e4. doi: 10.1093/pcp/pcs186. Epub 2013 Jan 3.

PMID:
23292603
2.

KNApSAcK family databases: integrated metabolite-plant species databases for multifaceted plant research.

Afendi FM, Okada T, Yamazaki M, Hirai-Morita A, Nakamura Y, Nakamura K, Ikeda S, Takahashi H, Altaf-Ul-Amin M, Darusman LK, Saito K, Kanaya S.

Plant Cell Physiol. 2012 Feb;53(2):e1. doi: 10.1093/pcp/pcr165. Epub 2011 Nov 28.

PMID:
22123792
3.

KNApSAcK Metabolite Activity Database for retrieving the relationships between metabolites and biological activities.

Nakamura Y, Afendi FM, Parvin AK, Ono N, Tanaka K, Hirai Morita A, Sato T, Sugiura T, Altaf-Ul-Amin M, Kanaya S.

Plant Cell Physiol. 2014 Jan;55(1):e7. doi: 10.1093/pcp/pct176. Epub 2013 Nov 27.

PMID:
24285751
4.

PRIMe Update: innovative content for plant metabolomics and integration of gene expression and metabolite accumulation.

Sakurai T, Yamada Y, Sawada Y, Matsuda F, Akiyama K, Shinozaki K, Hirai MY, Saito K.

Plant Cell Physiol. 2013 Feb;54(2):e5. doi: 10.1093/pcp/pcs184. Epub 2013 Jan 3.

5.

PRIMe: a Web site that assembles tools for metabolomics and transcriptomics.

Akiyama K, Chikayama E, Yuasa H, Shimada Y, Tohge T, Shinozaki K, Hirai MY, Sakurai T, Kikuchi J, Saito K.

In Silico Biol. 2008;8(3-4):339-45.

PMID:
19032166
6.

Differential metabolomics unraveling light/dark regulation of metabolic activities in Arabidopsis cell culture.

Nakamura Y, Kimura A, Saga H, Oikawa A, Shinbo Y, Kai K, Sakurai N, Suzuki H, Kitayama M, Shibata D, Kanaya S, Ohta D.

Planta. 2007 Dec;227(1):57-66. Epub 2007 Aug 15.

PMID:
17701204
7.

Metabolic profiling using Fourier-transform ion-cyclotron-resonance mass spectrometry.

Ohta D, Shibata D, Kanaya S.

Anal Bioanal Chem. 2007 Nov;389(5):1469-75. Epub 2007 Oct 6.

PMID:
17922113
8.

TIPdb-3D: the three-dimensional structure database of phytochemicals from Taiwan indigenous plants.

Tung CW, Lin YC, Chang HS, Wang CC, Chen IS, Jheng JL, Li JH.

Database (Oxford). 2014 Jun 13;2014. pii: bau055. doi: 10.1093/database/bau055. Print 2014.

9.

How large is the metabolome? A critical analysis of data exchange practices in chemistry.

Kind T, Scholz M, Fiehn O.

PLoS One. 2009;4(5):e5440. doi: 10.1371/journal.pone.0005440. Epub 2009 May 5.

10.

Three-dimensional structure database of natural metabolites (3DMET): a novel database of curated 3D structures.

Maeda MH, Kondo K.

J Chem Inf Model. 2013 Mar 25;53(3):527-33. doi: 10.1021/ci300309k. Epub 2013 Mar 7.

PMID:
23293959
11.

Systematization of the protein sequence diversity in enzymes related to secondary metabolic pathways in plants, in the context of big data biology inspired by the KNApSAcK motorcycle database.

Ikeda S, Abe T, Nakamura Y, Kibinge N, Hirai Morita A, Nakatani A, Ono N, Ikemura T, Nakamura K, Altaf-Ul-Amin M, Kanaya S.

Plant Cell Physiol. 2013 May;54(5):711-27. doi: 10.1093/pcp/pct041. Epub 2013 Mar 18.

PMID:
23509110
12.

In silico enzymatic synthesis of a 400,000 compound biochemical database for nontargeted metabolomics.

Menikarachchi LC, Hill DW, Hamdalla MA, Mandoiu II, Grant DF.

J Chem Inf Model. 2013 Sep 23;53(9):2483-92. doi: 10.1021/ci400368v. Epub 2013 Sep 12.

13.

PDTD: a web-accessible protein database for drug target identification.

Gao Z, Li H, Zhang H, Liu X, Kang L, Luo X, Zhu W, Chen K, Wang X, Jiang H.

BMC Bioinformatics. 2008 Feb 19;9:104. doi: 10.1186/1471-2105-9-104.

14.

MetAssimulo: simulation of realistic NMR metabolic profiles.

Muncey HJ, Jones R, De Iorio M, Ebbels TM.

BMC Bioinformatics. 2010 Oct 6;11:496. doi: 10.1186/1471-2105-11-496.

15.

Plant metabolomics: from experimental design to knowledge extraction.

Rai A, Umashankar S, Swarup S.

Methods Mol Biol. 2013;1069:279-312. doi: 10.1007/978-1-62703-613-9_19.

PMID:
23996322
16.

Web-based resources for mass-spectrometry-based metabolomics: a user's guide.

Tohge T, Fernie AR.

Phytochemistry. 2009 Mar;70(4):450-6. doi: 10.1016/j.phytochem.2009.02.004. Epub 2009 Mar 13. Review.

PMID:
19285697
17.

Assessment of metabolome annotation quality: a method for evaluating the false discovery rate of elemental composition searches.

Matsuda F, Shinbo Y, Oikawa A, Hirai MY, Fiehn O, Kanaya S, Saito K.

PLoS One. 2009 Oct 16;4(10):e7490. doi: 10.1371/journal.pone.0007490.

18.

Plant metabolomics--meeting the analytical challenges of comprehensive metabolite analysis.

Hegeman AD.

Brief Funct Genomics. 2010 Mar;9(2):139-48. doi: 10.1093/bfgp/elp053. Epub 2010 Jan 11. Review.

PMID:
20064859
19.

Combined 3D QSAR and molecular docking studies to reveal novel cannabinoid ligands with optimum binding activity.

Durdagi S, Papadopoulos MG, Papahatjis DP, Mavromoustakos T.

Bioorg Med Chem Lett. 2007 Dec 15;17(24):6754-63. Epub 2007 Oct 17.

PMID:
17980589
20.

Molecular docking and 3D-QSAR studies on the binding mechanism of statine-based peptidomimetics with beta-secretase.

Zuo Z, Luo X, Zhu W, Shen J, Shen X, Jiang H, Chen K.

Bioorg Med Chem. 2005 Mar 15;13(6):2121-31.

PMID:
15727865
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