Exploring designability of electrostatic complementarity at an antigen-antibody interface directed by mutagenesis, biophysical analysis, and molecular dynamics simulations
Yoshida, Kouhei, Kuroda, Daisuke, Kiyoshi, Masato, Nakakido, Makoto, Nagatoishi, Satoru, Soga, Shinji, Shirai, Hiroki, Tsumoto, Kouhei
Published in Scientific reports (14.03.2019)
Published in Scientific reports (14.03.2019)
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Journal Article
Structural classification of CDR-H3 revisited: A lesson in antibody modeling
Kuroda, Daisuke, Shirai, Hiroki, Kobori, Masato, Nakamura, Haruki
Published in Proteins, structure, function, and bioinformatics (15.11.2008)
Published in Proteins, structure, function, and bioinformatics (15.11.2008)
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Journal Article
Use of Amino Acid Composition to Predict Ligand-Binding Sites
Soga, Shinji, Shirai, Hiroki, Kobori, Masato, Hirayama, Noriaki
Published in Journal of chemical information and modeling (01.03.2007)
Published in Journal of chemical information and modeling (01.03.2007)
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Journal Article
Kotai Antibody Builder: automated high-resolution structural modeling of antibodies
Yamashita, Kazuo, Ikeda, Kazuyoshi, Amada, Karlou, Liang, Shide, Tsuchiya, Yuko, Nakamura, Haruki, Shirai, Hiroki, Standley, Daron M
Published in Bioinformatics (Oxford, England) (15.11.2014)
Published in Bioinformatics (Oxford, England) (15.11.2014)
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Journal Article
Affinity improvement of a therapeutic antibody by structure-based computational design: generation of electrostatic interactions in the transition state stabilizes the antibody-antigen complex
Kiyoshi, Masato, Caaveiro, Jose M M, Miura, Eri, Nagatoishi, Satoru, Nakakido, Makoto, Soga, Shinji, Shirai, Hiroki, Kawabata, Shigeki, Tsumoto, Kouhei
Published in PloS one (27.01.2014)
Published in PloS one (27.01.2014)
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Journal Article
High-resolution modeling of antibody structures by a combination of bioinformatics, expert knowledge, and molecular simulations
Shirai, Hiroki, Ikeda, Kazuyoshi, Yamashita, Kazuo, Tsuchiya, Yuko, Sarmiento, Jamica, Liang, Shide, Morokata, Tatsuaki, Mizuguchi, Kenji, Higo, Junichi, Standley, Daron M., Nakamura, Haruki
Published in Proteins, structure, function, and bioinformatics (01.08.2014)
Published in Proteins, structure, function, and bioinformatics (01.08.2014)
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Journal Article
Phase 1b randomized trial and follow-up study in Uganda of the blood-stage malaria vaccine candidate BK-SE36
Palacpac, Nirianne Marie Q, Ntege, Edward, Yeka, Adoke, Balikagala, Betty, Suzuki, Nahoko, Shirai, Hiroki, Yagi, Masanori, Ito, Kazuya, Fukushima, Wakaba, Hirota, Yoshio, Nsereko, Christopher, Okada, Takuya, Kanoi, Bernard N, Tetsutani, Kohhei, Arisue, Nobuko, Itagaki, Sawako, Tougan, Takahiro, Ishii, Ken J, Ueda, Shigeharu, Egwang, Thomas G, Horii, Toshihiro
Published in PloS one (28.05.2013)
Published in PloS one (28.05.2013)
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Journal Article
Use of amino acid composition to predict epitope residues of individual antibodies
Soga, Shinji, Kuroda, Daisuke, Shirai, Hiroki, Kobori, Masato, Hirayama, Noriaki
Published in Protein engineering, design and selection (01.06.2010)
Published in Protein engineering, design and selection (01.06.2010)
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Journal Article
Evidences of protection against blood-stage infection of Plasmodium falciparum by the novel protein vaccine SE36
Horii, Toshihiro, Shirai, Hiroki, Jie, Li, Ishii, Ken J, Palacpac, Nirianne Q, Tougan, Takahiro, Hato, Mariko, Ohta, Nobuo, Bobogare, Albino, Arakaki, Nana, Matsumoto, Yoshitsugu, Namazue, Junko, Ishikawa, Toyokazu, Ueda, Shigeharu, Takahashi, Michiaki
Published in Parasitology international (01.09.2010)
Published in Parasitology international (01.09.2010)
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Journal Article
Antibody titres and boosting after natural malaria infection in BK-SE36 vaccine responders during a follow-up study in Uganda
Yagi, Masanori, Palacpac, Nirianne M Q, Ito, Kazuya, Oishi, Yuko, Itagaki, Sawako, Balikagala, Betty, Ntege, Edward H, Yeka, Adoke, Kanoi, Bernard N, Katuro, Osbert, Shirai, Hiroki, Fukushima, Wakaba, Hirota, Yoshio, Egwang, Thomas G, Horii, Toshihiro
Published in Scientific reports (05.10.2016)
Published in Scientific reports (05.10.2016)
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Journal Article
Wide distribution of O157-antigen biosynthesis gene clusters in Escherichia coli
Iguchi, Atsushi, Shirai, Hiroki, Seto, Kazuko, Ooka, Tadasuke, Ogura, Yoshitoshi, Hayashi, Tetsuya, Osawa, Kayo, Osawa, Ro
Published in PloS one (18.08.2011)
Published in PloS one (18.08.2011)
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Journal Article
Computational design, construction, and characterization of a set of specificity determining residues in protein-protein interactions
Nagao, Chioko, Izako, Nozomi, Soga, Shinji, Khan, Samia Haseeb, Kawabata, Shigeki, Shirai, Hiroki, Mizuguchi, Kenji
Published in Proteins, structure, function, and bioinformatics (01.10.2012)
Published in Proteins, structure, function, and bioinformatics (01.10.2012)
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Journal Article
Identification of the Druggable Concavity in Homology Models Using the PLB Index
Soga, Shinji, Shirai, Hiroki, Kobori, Masato, Hirayama, Noriaki
Published in Journal of chemical information and modeling (01.11.2007)
Published in Journal of chemical information and modeling (01.11.2007)
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Journal Article
Modulation of O-antigen chain length by the wzz gene in Escherichia coli O157 influences its sensitivities to serum complement
Osawa, Kayo, Shigemura, Katsumi, Iguchi, Atsushi, Shirai, Hiroki, Imayama, Toru, Seto, Kazuko, Raharjo, Dadik, Fujisawa, Masato, Osawa, Ro, Shirakawa, Toshiro
Published in Microbiology and immunology (01.09.2013)
Published in Microbiology and immunology (01.09.2013)
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Association of naturally acquired IgG antibodies against Plasmodium falciparum serine repeat antigen-5 with reduced placental parasitemia and normal birth weight in pregnant Ugandan women: A pilot study
Owalla, Tonny J, Palacpac, Nirianne Marie Q, Shirai, Hiroki, Horii, Toshihiro, Egwang, Thomas G
Published in Parasitology international (01.06.2013)
Published in Parasitology international (01.06.2013)
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