"Tomii, K.,Motono, C.,Sato, M.,Ota, M.,Hirokawa, T.,Horton, P.,Akiyama, Y.","Andante - Tertiary Structure Prediction of CASP7 Targets Using Exhaustive Modeling and Evaluation",,"Proc. of Critical Assesment of Techniques for Protein Structure Prediction Seventh Meeting (CASP7)",,,,"pp. 14",2006,Dec.
"富井健太郎,本野千恵,佐藤美和,太田元規,酒谷尚文,藤原康広,三十尾潔高,広川貴次,Paul Horton,秋山 泰","立体構造予測実験CASP7に対するとり組み",,"CBRC 2006 予稿集 B5",,,,,2006,Sept.
"A. Mukaiyama,M. Haruki,M. Ota,Y. Koga,K. Takano,S. Kanaya","A hyperthermophilic protein acquires function at the cost of stability",,"Biochemistry",,"Vol. 24",,"pp. 12673-12679",2006,
"太田元規","立体構造予測，フォールド認識，経験的ポテンシャル関数",,"「バイオインフォマティクス事典」 日本バイオインフォマティクス学会編","共立出版",,,,2006,
"太田元規","特集：タンパク質機能解析に役立つデータベースとウェッブツール",,"バイオテクノロジージャーナル","羊土社","Vol. 6",,"pp. 426-456",2006,
"太田元規","タンパク質の立体構造予測",,"「複雑系の構造と予測」早稲田大学複雑系高等学術研究所 編","共立出版",,,,2006,
"Motonori Ota","Stabilization of E. coli ribonuclease HI by the 'stability profile of mutant protein' (SPMP)-inspired random and non-random mutagenesis",,"J. Biotech",,"Vol. 25",,"pp. 512-522",2006,
"太田元規","タンパク質フォールディング博物学の曙",,"生物物理",,"Vol. 266",,"pp. 224-227",2006,
"Motonori Ota","A hyperthermophilic protein acquires function at the cost of stability",,"Biochemistry",,"Vol. 24",,"pp. 12673-12679",2006,
"太田元規","タンパク質の分子設計",,,"「生物工学ハンドブック」コロナ社",,,,2005,Aug.
"Y. Isogai,Y. Ito,T. Ikeya,Y. Shiro,M. Ota","Design of lambda Cro Fold: Solution Structure of a Monomeric Variant of the De Novo Protein",,"J. Mol. Biol.",,"Vol. 354",,"pp. 801-814",2005,
"Y. Asada,M. Sawano,K. Ogasahara,J. Nakamura,M. Ota,C. Kuroishi,M. Sugahara,K. Yutani,N. Kunishima","Stabilization mechanism of the tryptophan synthase alpha-subunit from Thermus thermophilus HB8: X-ray crystallographic analysis and calorimetry",,"J. Biochem (Tokyo)",,"Vol. 138",,"pp. 343-353",2005,
"K. Kinoshita,M. Ota","P-cats: Prediction of catalytic residues in proteins from the tertiary structures",,"Bioinformatics",,"Vol. 21",,"pp. 3570-3571",2005,
"Y. Hioki,K. Ogasahara K,S. Lee,J. Ma,M. Ishida,Y. Yamagata,Y. Matsuura,M. Ota,M. Ikeguchi,S. Kuramitsu,K. Yutani","The crystal structure of the tryptophan synthase beta subunit from the hyperthermophile Pyrococcus furiosus",,"Eur. J. Biochem.",,"Vol. 271",,"pp. 2624-2635",2004,
"M. Ota,K. Kinoshita,K. Nishikawa","Prediction of catalytic residues in enzymes based on known tertiary structure, stability profile, and sequence conservation",,"J. Mol. Biol.",,"Vol. 327",,"pp. 1053-1064",2003,
"T. Aita,M. Ota,Y. Husimi","An in silico exploration of the neutral network in protein sequence space",,"J. Theor. Biol.",,"Vol. 221",,"pp. 599-613",2003,
"N. Handa,T. Terada,Y. Kamewari,H. Hamana,J. R. H. Tame,S.-Y. Park,K. Kinoshita,M. Ota,H. Nakamura,S. Kuramitsu,M. Shirouzu,S. Yokoyama","Crystal structure of the conserved protein TT1542 from Thermus thermophilus HB8",,"Protein Sci.",,"Vol. 12",,"pp. 1621-1632",2003,
"太田元規","タンパク質の理論構造生物学",,"「生命情報学」シュプリンガー・フェアラーク東京","「生命情報学」シュプリンガー・フェアラーク東京",,,"pp. 109-149",2003,
"太田元規","タンパク質立体構造のバイオインフォマティクス",,"「バイオインフォマティクスがわかる」羊土社","「バイオインフォマティクスがわかる」羊土社",,,,2003,
"太田元規","アミノ酸配列から立体構造を予測する",,"蛋白質核酸酵素",,"Vol. 47",,"pp. 181-186",2002,
"太田元規","アミノ酸配列から二次構造を予測する",,"蛋白質核酸酵素",,"Vol. 47",,"pp. 85-90",2002,
"K.Homma,S. Fukuchi,T. Kawabata,M. Ota,K. Nishikawa","A systematic investigation identifies a significant number of probable pseudogenes in the Echerichia coli genome",,"Gene",,"Vol. 294",,"pp. 25-33",2002,
"T. Kawabata,S. Fukuchi,K. Homma,M. Ota,J. Araki,T. Ito,N. Ichiyoshi,K. Nishikawa","GTOP: a database of protein structures predicted from genome sequences.",,"Nucleic Acid Res.",,"Vol. 30",,"pp. 294-298",2002,
"Y. Isogai,M. Ota,A. Ishii,M. Ishida,K. Nishikawa","Identification of amino acids involved in protein structural uniqueness: implication for de novo protein design",,"Protein Eng.",,"Vol. 15",,"pp. 555-560",2002,
"太田元規","アミノ酸配列から２次構造を予測する　アミノ酸配列から立体構造を予測する",,"「あなたにも役立つバイオインフォマティクス」共立出版","「あなたにも役立つバイオインフォマティクス」共立出版",,,,2002,
"太田元規,西川建","タンパク質高次構造の予測",,"「プロテオミクスの基礎」講談社サイエンティフィク","「プロテオミクスの基礎」講談社サイエンティフィク",,,,2001,
"磯貝泰弘,太田元規","人工タンパク質の合理的設計",,"シリーズ・ニューバイオフィジックス９巻「生体ナノマシンの分子設計」共立出版","シリーズ・ニューバイオフィジックス９巻「生体ナノマシンの分子設計」共立出版",,,,2001,
"M. Ota,K. Nishikawa","Feasibility in the inverse protein folding protocol",,"Protein Sci.",,"Vol. 8",,"pp. 1001-1009",1999,
"Y. Isogai,M. Ota et al.","Design and synthesis of a globin fold",,"Biochemistry",,"Vol. 38",,"pp. 7431-7443",1999,
"太田元規","Protein structure-sequence compatibility search",,,,,,,1996,
"M. Ota,S. Kanaya,K. Nishikawa","Desk-top analysis of the structural stabilities of various point mutations introduced into ribonuclrease H",,"J. Mol. Biol.",,"Vol. 248",,"pp. 733-738",1995,
"太田元規","島模型―キリンを三工程で冷蔵庫に入れる方法",,"「遺伝子情報処理への挑戦」共立出版","「遺伝子情報処理への挑戦」共立出版",,,,1994,