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Items: 1 to 50 of 129

1.

Novel Antifungal Compound Z-705 Specifically Inhibits Protein Kinase C of Filamentous Fungi.

Sugahara A, Yoshimi A, Shoji F, Fujioka T, Kawai K, Umeyama H, Komatsu K, Enomoto M, Kuwahara S, Hagiwara D, Katayama T, Horiuchi H, Miyazawa K, Nakayama M, Abe K.

Appl Environ Microbiol. 2019 May 2;85(10). pii: e02923-18. doi: 10.1128/AEM.02923-18. Print 2019 May 15.

PMID:
30902853
2.

Ubiquitin-dependent proteolysis of CXCL7 leads to posterior longitudinal ligament ossification.

Tsuru M, Ono A, Umeyama H, Takeuchi M, Nagata K.

PLoS One. 2018 May 21;13(5):e0196204. doi: 10.1371/journal.pone.0196204. eCollection 2018.

3.

Retrospective Proteomic Analysis of a Novel, Cancer Metastasis-Promoting RGD-Containing Peptide.

Tsuru M, Sata M, Tanaka M, Umeyama H, Kodera Y, Shiwa M, Aoyagi N, Yasuda K, Matsuoka K, Fukuda T, Yamana H, Nagata K.

Transl Oncol. 2017 Dec;10(6):998-1007. doi: 10.1016/j.tranon.2017.10.001. Epub 2017 Nov 2.

4.

An iterative compound screening contest method for identifying target protein inhibitors using the tyrosine-protein kinase Yes.

Chiba S, Ishida T, Ikeda K, Mochizuki M, Teramoto R, Taguchi YH, Iwadate M, Umeyama H, Ramakrishnan C, Thangakani AM, Velmurugan D, Gromiha MM, Okuno T, Kato K, Minami S, Chikenji G, Suzuki SD, Yanagisawa K, Shin WH, Kihara D, Yamamoto KZ, Moriwaki Y, Yasuo N, Yoshino R, Zozulya S, Borysko P, Stavniichuk R, Honma T, Hirokawa T, Akiyama Y, Sekijima M.

Sci Rep. 2017 Sep 20;7(1):12038. doi: 10.1038/s41598-017-10275-4.

5.

Core I97L mutation in conjunction with P79Q is associated with persistent low HBV DNA and HBs antigen clearance in patients with chronic hepatitis B.

Honda T, Ishigami M, Ishizu Y, Kuzuya T, Hayashi K, Ishikawa T, Murakami Y, Iwadate M, Umeyama H, Toyoda H, Kumada T, Katano Y, Goto H, Hirooka Y.

Clin Microbiol Infect. 2017 Jun;23(6):407.e1-407.e7. doi: 10.1016/j.cmi.2016.12.014. Epub 2016 Dec 18.

6.

Molecular Dynamics Simulations to Determine the Structure and Dynamics of Hepatitis B Virus Capsid Bound to a Novel Anti-viral Drug.

Watanabe G, Sato S, Iwadate M, Umeyama H, Hayakawa M, Murakami Y, Yoneda S.

Chem Pharm Bull (Tokyo). 2016;64(9):1393-6. doi: 10.1248/cpb.c16-00132.

7.

SFRP1 is a possible candidate for epigenetic therapy in non-small cell lung cancer.

Taguchi YH, Iwadate M, Umeyama H.

BMC Med Genomics. 2016 Aug 12;9 Suppl 1:28. doi: 10.1186/s12920-016-0196-3.

8.

Inhibition of bacterial undecaprenyl pyrophosphate synthase by small fungal molecules.

Inokoshi J, Nakamura Y, Komada S, Komatsu K, Umeyama H, Tomoda H.

J Antibiot (Tokyo). 2016 Nov;69(11):798-805. doi: 10.1038/ja.2016.35. Epub 2016 Apr 6.

PMID:
27049441
9.

Identification of potential inhibitors based on compound proposal contest: Tyrosine-protein kinase Yes as a target.

Chiba S, Ikeda K, Ishida T, Gromiha MM, Taguchi YH, Iwadate M, Umeyama H, Hsin KY, Kitano H, Yamamoto K, Sugaya N, Kato K, Okuno T, Chikenji G, Mochizuki M, Yasuo N, Yoshino R, Yanagisawa K, Ban T, Teramoto R, Ramakrishnan C, Thangakani AM, Velmurugan D, Prathipati P, Ito J, Tsuchiya Y, Mizuguchi K, Honma T, Hirokawa T, Akiyama Y, Sekijima M.

Sci Rep. 2015 Nov 26;5:17209. doi: 10.1038/srep17209.

10.

Development of novel hepatitis B virus capsid inhibitor using in silico screening.

Hayakawa M, Umeyama H, Iwadate M, Tanahashi T, Yano Y, Enomoto M, Tamori A, Kawada N, Murakami Y.

Biochem Biophys Res Commun. 2015 Aug 7;463(4):1165-75. doi: 10.1016/j.bbrc.2015.06.077. Epub 2015 Jun 18.

PMID:
26095852
11.
12.

TINAGL1 and B3GALNT1 are potential therapy target genes to suppress metastasis in non-small cell lung cancer.

Umeyama H, Iwadate M, Taguchi YH.

BMC Genomics. 2014;15 Suppl 9:S2. doi: 10.1186/1471-2164-15-S9-S2. Epub 2014 Dec 8.

13.

Discovering novel direct acting antiviral agents for HBV using in silico screening.

Murakami Y, Hayakawa M, Yano Y, Tanahashi T, Enomoto M, Tamori A, Kawada N, Iwadate M, Umeyama H.

Biochem Biophys Res Commun. 2015 Jan 2;456(1):20-8. doi: 10.1016/j.bbrc.2014.11.024. Epub 2014 Nov 15.

PMID:
25446116
14.

Genes associated with genotype-specific DNA methylation in squamous cell carcinoma as candidate drug targets.

Kinoshita R, Iwadate M, Umeyama H, Taguchi YH.

BMC Syst Biol. 2014;8 Suppl 1:S4. doi: 10.1186/1752-0509-8-S1-S4. Epub 2014 Jan 24.

15.
16.

Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions.

Moretti R, Fleishman SJ, Agius R, Torchala M, Bates PA, Kastritis PL, Rodrigues JP, Trellet M, Bonvin AM, Cui M, Rooman M, Gillis D, Dehouck Y, Moal I, Romero-Durana M, Perez-Cano L, Pallara C, Jimenez B, Fernandez-Recio J, Flores S, Pacella M, Praneeth Kilambi K, Gray JJ, Popov P, Grudinin S, Esquivel-Rodríguez J, Kihara D, Zhao N, Korkin D, Zhu X, Demerdash ON, Mitchell JC, Kanamori E, Tsuchiya Y, Nakamura H, Lee H, Park H, Seok C, Sarmiento J, Liang S, Teraguchi S, Standley DM, Shimoyama H, Terashi G, Takeda-Shitaka M, Iwadate M, Umeyama H, Beglov D, Hall DR, Kozakov D, Vajda S, Pierce BG, Hwang H, Vreven T, Weng Z, Huang Y, Li H, Yang X, Ji X, Liu S, Xiao Y, Zacharias M, Qin S, Zhou HX, Huang SY, Zou X, Velankar S, Janin J, Wodak SJ, Baker D.

Proteins. 2013 Nov;81(11):1980-7. doi: 10.1002/prot.24356. Epub 2013 Aug 23.

17.

A new method for induced fit docking (GENIUS) and its application to virtual screening of novel HCV NS3-4A protease inhibitors.

Takaya D, Yamashita A, Kamijo K, Gomi J, Ito M, Maekawa S, Enomoto N, Sakamoto N, Watanabe Y, Arai R, Umeyama H, Honma T, Matsumoto T, Yokoyama S.

Bioorg Med Chem. 2011 Nov 15;19(22):6892-905. doi: 10.1016/j.bmc.2011.09.023. Epub 2011 Sep 16.

PMID:
21992802
18.

Human liver enzymes responsible for metabolic elimination of tyramine; a vasopressor agent from daily food.

Niwa T, Murayama N, Umeyama H, Shimizu M, Yamazaki H.

Drug Metab Lett. 2011 Aug;5(3):216-9.

PMID:
21679153
19.

New protein structure model evaluation methods that include a side-chain consensus score for the protein modeling.

Kanou K, Hirata T, Terashi G, Umeyama H, Takeda-Shitaka M.

Chem Pharm Bull (Tokyo). 2010 Feb;58(2):180-90.

20.

HUMAN FAMSD-BASE: high quality protein structure model database for the human genome using the FAMSD homology modeling method.

Kanou K, Hirata T, Iwadate M, Terashi G, Umeyama H, Takeda-Shitaka M.

Chem Pharm Bull (Tokyo). 2010 Jan;58(1):66-75.

21.

Method for predicting homology modeling accuracy from amino acid sequence alignment: the power function.

Iwadate M, Kanou K, Terashi G, Umeyama H, Takeda-Shitaka M.

Chem Pharm Bull (Tokyo). 2010 Jan;58(1):1-10.

22.

FAMSD: A powerful protein modeling platform that combines alignment methods, homology modeling, 3D structure quality estimation and molecular dynamics.

Kanou K, Iwadate M, Hirata T, Terashi G, Umeyama H, Takeda-Shitaka M.

Chem Pharm Bull (Tokyo). 2009 Dec;57(12):1335-42.

23.
24.

Mechanism by which the lectin actinohivin blocks HIV infection of target cells.

Tanaka H, Chiba H, Inokoshi J, Kuno A, Sugai T, Takahashi A, Ito Y, Tsunoda M, Suzuki K, Takénaka A, Sekiguchi T, Umeyama H, Hirabayashi J, Omura S.

Proc Natl Acad Sci U S A. 2009 Sep 15;106(37):15633-8. doi: 10.1073/pnas.0907572106. Epub 2009 Aug 26.

25.

Bioinformatics based Ligand-Docking and in-silico screening.

Takaya D, Takeda-Shitaka M, Terashi G, Kanou K, Iwadate M, Umeyama H.

Chem Pharm Bull (Tokyo). 2008 May;56(5):742-4.

26.
27.

FAMS and FAMSBASE for protein structure.

Umeyama H, Iwadate M.

Curr Protoc Bioinformatics. 2004 Feb;Chapter 5:Unit5.2. doi: 10.1002/0471250953.bi0502s04.

PMID:
18428727
28.

Fams-ace: a combined method to select the best model after remodeling all server models.

Terashi G, Takeda-Shitaka M, Kanou K, Iwadate M, Takaya D, Hosoi A, Ohta K, Umeyama H.

Proteins. 2007;69 Suppl 8:98-107.

PMID:
17894329
29.

The SKE-DOCK server and human teams based on a combined method of shape complementarity and free energy estimation.

Terashi G, Takeda-Shitaka M, Kanou K, Iwadate M, Takaya D, Umeyama H.

Proteins. 2007 Dec 1;69(4):866-72.

PMID:
17853449
30.

[Three-dimensional structure prediction of the viral protein in the development of anti SARS drugs].

Takeda-Shitaka M, Umeyama H.

Tanpakushitsu Kakusan Koso. 2007 Aug;52(10 Suppl):1082-7. Japanese. No abstract available.

PMID:
17824221
31.

Topology of AspT, the aspartate:alanine antiporter of Tetragenococcus halophilus, determined by site-directed fluorescence labeling.

Nanatani K, Fujiki T, Kanou K, Takeda-Shitaka M, Umeyama H, Ye L, Wang X, Nakajima T, Uchida T, Maloney PC, Abe K.

J Bacteriol. 2007 Oct;189(19):7089-97. Epub 2007 Jul 27.

32.

Regioselective cycloaddition reaction of alkene molecules with the asymmetric dimer on Si(100)c(4 x 2).

Oguchi K, Nagao M, Umeyama H, Katayama T, Yamashita Y, Mukai K, Yoshinobu J, Akagi K, Tsuneyuki S.

J Am Chem Soc. 2007 Feb 7;129(5):1242-5.

PMID:
17263407
33.

Identification of amino acid residues of Salmonella SlyA that are critical for transcriptional regulation.

Okada N, Oi Y, Takeda-Shitaka M, Kanou K, Umeyama H, Haneda T, Miki T, Hosoya S, Danbara H.

Microbiology. 2007 Feb;153(Pt 2):548-60.

PMID:
17259627
34.

FAMS complex: a fully automated homology modeling system for protein complex structures.

Takeda-Shitaka M, Terashi G, Chiba C, Takaya D, Umeyama H.

Med Chem. 2006 Mar;2(2):191-201.

PMID:
16787367
35.

Protein structure prediction in CASP6 using CHIMERA and FAMS.

Takeda-Shitaka M, Terashi G, Takaya D, Kanou K, Iwadate M, Umeyama H.

Proteins. 2005;61 Suppl 7:122-7.

PMID:
16187353
36.
37.

Remarkably different structures and reaction mechanisms of ketoreductases for the opposite stereochemical control in the biosynthesis of BIQ antibiotics.

Taguchi T, Kunieda K, Takeda-Shitaka M, Takaya D, Kawano N, Kimberley MR, Booker-Milburn KI, Stephenson GR, Umeyama H, Ebizuka Y, Ichinose K.

Bioorg Med Chem. 2004 Nov 15;12(22):5917-27.

PMID:
15498668
38.

Precursor mediated cycloaddition reaction of ethylene to the Si(100)c(4 x 2) surface.

Nagao M, Umeyama H, Mukai K, Yamashita Y, Yoshinobu J, Akagi K, Tsuneyuki S.

J Am Chem Soc. 2004 Aug 18;126(32):9922-3.

PMID:
15303857
39.

Evaluation of homology modeling of the severe acute respiratory syndrome (SARS) coronavirus main protease for structure based drug design.

Takeda-Shitaka M, Nojima H, Takaya D, Kanou K, Iwadate M, Umeyama H.

Chem Pharm Bull (Tokyo). 2004 May;52(5):643-5.

40.

Protein structure prediction in structure based drug design.

Takeda-Shitaka M, Takaya D, Chiba C, Tanaka H, Umeyama H.

Curr Med Chem. 2004 Mar;11(5):551-8. Review.

PMID:
15032603
41.

Molecular characterization of ADAMTS13 gene mutations in Japanese patients with Upshaw-Schulman syndrome.

Matsumoto M, Kokame K, Soejima K, Miura M, Hayashi S, Fujii Y, Iwai A, Ito E, Tsuji Y, Takeda-Shitaka M, Iwadate M, Umeyama H, Yagi H, Ishizashi H, Banno F, Nakagaki T, Miyata T, Fujimura Y.

Blood. 2004 Feb 15;103(4):1305-10. Epub 2003 Oct 16.

42.

Interaction between the antigen and antibody is controlled by the constant domains: normal mode dynamics of the HEL-HyHEL-10 complex.

Adachi M, Kurihara Y, Nojima H, Takeda-Shitaka M, Kamiya K, Umeyama H.

Protein Sci. 2003 Oct;12(10):2125-31.

43.

Dynamic flexibility of a peptide-binding groove of human HLA-DR1 class II MHC molecules: normal mode analysis of the antigen peptide-class II MHC complex.

Nojima H, Takeda-Shitaka M, Kurihara Y, Kamiya K, Umeyama H.

Chem Pharm Bull (Tokyo). 2003 Aug;51(8):923-8.

44.

Dynamic character of human growth hormone and its receptor: normal mode analysis.

Kurihara Y, Watanabe T, Nojima H, Takeda-Shitaka M, Sumikawa H, Kamiya K, Umeyama H.

Chem Pharm Bull (Tokyo). 2003 Jul;51(7):754-8.

45.

Evaluation of the third solvent clusters fitting procedure for the prediction of protein-protein interactions based on the results at the CAPRI blind docking study.

Komatsu K, Kurihara Y, Iwadate M, Takeda-Shitaka M, Umeyama H; CAPRI blind docking study.

Proteins. 2003 Jul 1;52(1):15-8.

PMID:
12784361
46.

Algorithm for normal mode analysis with general internal coordinates.

Kamiya K, Sugawara Y, Umeyama H.

J Comput Chem. 2003 May;24(7):826-41.

PMID:
12692792
47.

Enlarged FAMSBASE: protein 3D structure models of genome sequences for 41 species.

Yamaguchi A, Iwadate M, Suzuki E, Yura K, Kawakita S, Umeyama H, Go M.

Nucleic Acids Res. 2003 Jan 1;31(1):463-8.

48.

[Modeling of all genome and database].

Umeyama H.

Nihon Yakurigaku Zasshi. 2002 Nov;120(1):43P-46P. Japanese.

PMID:
12491776
49.

Motion of an antiviral compound in a rhinovirus capsid under rotational symmetry boundary conditions.

Yoneda S, Yoneda T, Kurihara Y, Umeyama H.

J Mol Graph Model. 2002 Aug;21(1):19-27.

PMID:
12413027
50.

Dynamic characteristics of a peptide-binding groove of human HLA-A2 class I MHC molecules: normal mode analysis of the antigen peptide-class I MHC complex.

Nojima H, Takeda-Shitaka M, Kurihara Y, Adachi M, Yoneda S, Kamiya K, Umeyama H.

Chem Pharm Bull (Tokyo). 2002 Sep;50(9):1209-14.

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