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Papers authored by Umeyama H

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Dynamic Influence of the Two Membrane-Proximal Immunoglobulin-Like Domains upon the Peptide-Binding Platform Domain in Class I and Class II Major Histocompatibility Complexes: Normal Mode Analysis.

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Nojima H, Kanou K, Kamiya K, Atsuda K, Umeyama H, and Takeda-Shitaka M

Chemical & pharmaceutical bulletin 57(11):1193-9, 2009 Nov - Who cited this? | PubMed ID: 19881266 | Fulltext

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

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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, and Omura S

Proceedings of the National Academy of Sciences of the United States of America 106(37):15633-8, 2009 Sep 15 - Who cited this? | PubMed ID: 19717426 | Fulltext

Dynamic Interaction among the Platform Domain and Two Membrane-Proximal Immunoglobulin-Like Domains of Class I Major Histocompatibility Complex: Normal Mode Analysis.

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Nojima H, Takeda-Shitaka M, Kanou K, Kamiya K, and Umeyama H

Chemical & pharmaceutical bulletin 56(5):635-41, 2008 May - Who cited this? | PubMed ID: 18451549 | Fulltext

Bioinformatics Based Ligand-Docking and in-Silico Screening.

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

Chemical & pharmaceutical bulletin 56(5):742-4, 2008 May - Who cited this? | PubMed ID: 18451572 | Fulltext

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

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

Proteins 69(4):866-72, 2007 Dec 1 - Who cited this? | PubMed ID: 17853449 | Fulltext

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

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

Journal of bacteriology 189(19):7089, 2007 Oct - Who cited this? | PubMed ID: 17660287 | Fulltext

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

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Takeda-Shitaka M and Umeyama H

Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme 52(10 Suppl):1082-7, 2007 Aug - Who cited this? | PubMed ID: 17824221 | Fulltext

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

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

Journal of the American Chemical Society 129(5):1242-5, 2007 Feb 7 - Who cited this? | PubMed ID: 17263407 | Fulltext

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

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

Microbiology (Reading, England) 153(Pt 2):548, 2007 Feb - Who cited this? | PubMed ID: 17259627 | Fulltext

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

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

Proteins 69 Suppl 8:98-107, 2007 - Who cited this? | PubMed ID: 17894329 | Fulltext

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

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

Medicinal chemistry (Shariqah (United Arab Emirates)) 2(2):191-201, 2006 Mar - Who cited this? | PubMed ID: 16787367 | Fulltext

Searching for protein-protein interaction sites and docking by the methods of molecular dynamics, grid scoring, and the pairwise interaction potential of amino acid residues.

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Terashi G, Takeda-Shitaka M, Takaya D, Komatsu K, and Umeyama H

Proteins 60(2):289-95, 2005 Aug 1 - Who cited this? | PubMed ID: 15981245 | Fulltext

Protein structure prediction in CASP6 using CHIMERA and FAMS.

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

Proteins 61 Suppl 7:122-7, 2005 - Who cited this? | PubMed ID: 16187353 | Fulltext

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

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

Bioorganic & medicinal chemistry 12(22):5917-27, 2004 Nov 15 - Who cited this? | PubMed ID: 15498668 | Fulltext

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

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

Journal of the American Chemical Society 126(32):9922-3, 2004 Aug 18 - Who cited this? | PubMed ID: 15303857 | Fulltext

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

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

Chemical & pharmaceutical bulletin 52(5):643-5, 2004 May - Who cited this? | PubMed ID: 15133227 | Fulltext

Protein structure prediction in structure based drug design.

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

Current medicinal chemistry 11(5):551-8, 2004 Mar - Who cited this? | PubMed ID: 15032603 | Fulltext

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

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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,

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Blood 103(4):1305-10, 2004 Feb 15 - Who cited this? | PubMed ID: 14563640 | Fulltext

FAMS and FAMSBASE for protein structure.

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Umeyama H and Iwadate M

Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] Chapter 5:Unit5.2, 2004 Feb - Who cited this? | PubMed ID: 18428727 | Fulltext

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

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

Protein science : a publication of the Protein Society 12(10):2125-31, 2003 Oct - Who cited this? | PubMed ID: 14500870 | Fulltext

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.

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

Chemical & pharmaceutical bulletin 51(8):923-8, 2003 Aug - Who cited this? | PubMed ID: 12913229 | Fulltext

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

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

Chemical & pharmaceutical bulletin 51(7):754-8, 2003 Jul - Who cited this? | PubMed ID: 12843579 | Fulltext

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.

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

Proteins 52(1):15-8, 2003 Jul 1 - Who cited this? | PubMed ID: 12784361 | Fulltext

Algorithm for normal mode analysis with general internal coordinates.

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Kamiya K, Sugawara Y, and Umeyama H

Journal of computational chemistry 24(7):826-41, 2003 May - Who cited this? | PubMed ID: 12692792 | Fulltext

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

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

Nucleic acids research 31(1):463-8, 2003 Jan 1 - Who cited this? | PubMed ID: 12520053 | Fulltext

[Modeling of all genome and database].

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Umeyama H

Nippon yakurigaku zasshi. Folia pharmacologica Japonica 120(1):43P-46P, 2002 Nov - Who cited this? | PubMed ID: 12491776 | Fulltext

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.

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

Chemical & pharmaceutical bulletin 50(9):1209-14, 2002 Sep - Who cited this? | PubMed ID: 12237537 | Fulltext

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

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

Journal of molecular graphics & modelling 21(1):19-27, 2002 Aug - Who cited this? | PubMed ID: 12413027 | Fulltext

Substitution of Gly-548 to Ala in the substrate binding pocket of prothrombin Perijá leads to the loss of thrombin proteolytic activity.

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Sekine O, Sugo T, Ebisawa K, Umeyama H, Iwahana H, Ruiz-Sáez A, de Bosch N, and Matsudai M

Thrombosis and haemostasis 87(2):282-7, 2002 Feb - Who cited this? | PubMed ID: 11858488 | Fulltext

Augmentation of human immunodeficiency virus type 1 subtype E (CRF01_AE) multiple-drug resistance by insertion of a foreign 11-amino-acid fragment into the reverse transcriptase.

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Sato H, Tomita Y, Ebisawa K, Hachiya A, Shibamura K, Shiino T, Yang R, Tatsumi M, Gushi K, Umeyama H, Oka S, Takebe Y, and Nagai Y

Journal of virology 75(12):5604-13, 2001 Jun - Who cited this? | PubMed ID: 11356968 | Fulltext

An automatic homology modeling method consisting of database searches and simulated annealing.

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Ogata K and Umeyama H

Journal of molecular graphics & modelling 18(3):258-72, 305-6, 2000 Jun - Who cited this? | PubMed ID: 11021542 | Fulltext

Intermediate state during the crystal transition in aspartame, studied with thermal analysis, solid-state NMR, and molecular dynamics simulation.

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Ebisawa K, Nagashima N, Fukuhara K, Kumon S, Kishimoto S, Suzuki E, Yoneda S, and Umeyama H

Chemical & pharmaceutical bulletin 48(5):708-15, 2000 May - Who cited this? | PubMed ID: 10823710 | Fulltext

Dynamic character of the complex of human blood coagulation factor VIIa with the extracellular domain of human tissue factor: a normal mode analysis.

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Soejima K, Kurihara Y, Kamiya K, and Umeyama H

FEBS letters 463(1-2):19-23, 1999 Dec 10 - Who cited this? | PubMed ID: 10601630 | Fulltext

A homology modeling method of an icosahedral viral capsid: inclusion of surrounding protein structures.

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Yoneda T, Yoneda S, Takayama N, Kitazawa M, and Umeyama H

Journal of molecular graphics & modelling 17(2):114-9, 137-42, 1999 Apr - Who cited this? | PubMed ID: 10680117 | Fulltext

Structural studies of the interactions of normal and abnormal human plasmins with bovine basic pancreatic trypsin inhibitor.

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Takeda-Shitaka M, Kamiya K, Miyata T, Ohkura N, Madoiwa S, Sakata Y, and Umeyama H

Chemical & pharmaceutical bulletin 47(3):322-8, 1999 Mar - Who cited this? | PubMed ID: 10212382 | Fulltext

Factors X Nice I and II: two novel missense mutations (Met-40Val and Pro304Ser) in patient with coagulation factor X deficiency.

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Miyata T, Fischer F, Umeyama H, Appert A, Jambou D, and Kato H

Thrombosis and haemostasis 80(4):709-10, 1998 Oct - Who cited this? | PubMed ID: 9799000 | Fulltext

Effect of exceptional valine replacement for highly conserved alanine-55 on the catalytic site structure of chymotrypsin-like serine protease.

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Takeda-Shitaka M and Umeyama H

Chemical & pharmaceutical bulletin 46(9):1343-8, 1998 Sep - Who cited this? | PubMed ID: 9775431 | Fulltext

Dynamic structures of granulocyte colony-stimulating factor proteins studied by normal mode analysis: two domain-type motions in low frequency modes.

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Sumikawa H, Suzuki E, Fukuhara K, Nakajima Y, Kamiya K, and Umeyama H

Chemical & pharmaceutical bulletin 46(7):1069-77, 1998 Jul - Who cited this? | PubMed ID: 9692216 | Fulltext

The role played by environmental residues on sidechain torsional angles within homologous families of proteins: a new method of sidechain modeling.

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Ogata K and Umeyama H

Proteins 31(4):355-69, 1998 Jun 1 - Who cited this? | PubMed ID: 9626696 | Fulltext

The carboxyl-terminal region of protein C is essential for its secretion.

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Katsumi A, Kojima T, Senda T, Yamazaki T, Tsukamoto H, Sugiura I, Kobayashi S, Miyata T, Umeyama H, and Saito H

Blood 91(10):3784-91, 1998 May 15 - Who cited this? | PubMed ID: 9573015 | Fulltext

Arg260-Cys mutation in severe factor XIII deficiency: conformational change of the A subunit is predicted by molecular modelling and mechanics.

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Ichinose A, Tsukamoto H, Izumi T, Yamazaki T, Togashi M, Takamatsu J, Saito H, and Umeyama H

British journal of haematology 101(2):264-72, 1998 May - Who cited this? | PubMed ID: 9609521 | Fulltext

Molecular mechanisms of type II factor XIII deficiency: novel Gly562-Arg mutation and C-terminal truncation of the A subunit cause factor XIII deficiency as characterized in a mammalian expression system.

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Takahashi N, Tsukamoto H, Umeyama H, Castaman G, Rodeghiero F, and Ichinose A

Blood 91(8):2830-8, 1998 Apr 15 - Who cited this? | PubMed ID: 9531593 | Fulltext

Elucidation of the cause for reduced activity of abnormal human plasmin containing an Ala55-Thr mutation: importance of highly conserved Ala55 in serine proteases.

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Takeda-Shitaka M and Umeyama H

FEBS letters 425(3):448-52, 1998 Apr 3 - Who cited this? | PubMed ID: 9563511 | Fulltext

Factor X Nagoya 1 and Nagoya 2: a CRM- factor X deficiency and a dysfunctional CRM+ factor X deficiency characterized by substitution of Arg306 by Cys and of Gly366 by Ser, respectively.

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Miyata T, Kojima T, Suzuki K, Umeyama H, Yamazaki T, Kamiya T, Toyoda H, and Kato H

Thrombosis and haemostasis 79(3):486-90, 1998 Mar - Who cited this? | PubMed ID: 9531027 | Fulltext

Amino acid similarity matrix for homology modeling derived from structural alignment and optimized by the Monte Carlo method.

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Ogata K, Ohya M, and Umeyama H

Journal of molecular graphics & modelling 16(4-6):178-89, 254, 1998 - Who cited this? | PubMed ID: 10522237 | Fulltext

A computer modeling study of the interaction between tissue factor pathway inhibitor and blood coagulation factor Xa.

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Yoneda T, Komooka H, and Umeyama H

Journal of protein chemistry 16(6):597-605, 1997 Aug - Who cited this? | PubMed ID: 9263122 | Fulltext

A theoretical approach to the bell-shaped dependency of cell proliferation on the hormone concentration.

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Higo J and Umeyama H

Journal of theoretical biology 186(4):477-90, 1997 Jun 21 - Who cited this? | PubMed ID: 9278723 | Fulltext

Prediction of protein side-chain conformations by principal component analysis for fixed main-chain atoms.

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Ogata K and Umeyama H

Protein engineering 10(4):353-9, 1997 Apr - Who cited this? | PubMed ID: 9194159 | Fulltext

Protein dynamics determined by backbone conformation and atom packing.

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Higo J and Umeyama H

Protein engineering 10(4):373-80, 1997 Apr - Who cited this? | PubMed ID: 9194161 | Fulltext

Alanine exchanges of polar amino acids in the transmembrane domains of a platelet-activating factor receptor generate both constitutively active and inactive mutants.

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Ishii I, Izumi T, Tsukamoto H, Umeyama H, Ui M, and Shimizu T

The Journal of biological chemistry 272(12):7846-54, 1997 Mar 21 - Who cited this? | PubMed ID: 9065450 | Fulltext

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