PMD : 変異タンパク質データベース
Protein Mutant Database

K.Nishikawa, S.Ishino, H. Takenaka, N.Norioka, T.Hirai, T.Yao, and Y.Seto. "Constructing a protein mutant database". Protein Engineering. 7, 773, 1994.

GTOP : 全ゲノム立体構造予測データベース
Database of predicted protein structures from genome sequences

Takeshi Kawabata, Satoshi Fukuchi, Keiichi Homma, Motonori Ota, Jiro Araki, Takehiko Ito, Nobuyoshi Ichiyoshi & Ken Nishikawa. "GTOP: a database of protein structures predicted from genome sequences." Nuc. Acid Res. 30, 294-298, 2002.

TTDB : 転写・翻訳系タンパク質データベース
Transcription-Translation DataBase

GTOP-TF : 転写因子データベース
Database constructed by Automatic identification of Transcription Factors from Genome Sequences

Yoshiaki Minezaki, Keiichi Homma, and Ken Nishikawa "Genome-Wide Survey of Transcription Factors in Prokaryotes Reveals Many Bacteria-Specific Families Not Found in Archaea". DNA Research Advance Access published on January 10, 2006.

LIBRA I : 3D-1D法によるタンパク質の立体構造予測および配列解析
Protein structure-sequence compatibility analysis

Ota, M. and Nishikawa, K.: "Feasibility in the inverse protein folding protocol", Protein Sci. 8, 1001-1009, 1999.

GTOP構造予測 : PSI-BLASTによる立体構造予測
Reverse PSI-BLAST search against 3D-structure

CRNPRED : 臨界ランダムネットワークによるタンパク質の１次元構造予測（二次 構造・埋もれ度・残基毎コンタクトオーダ）
Prediction of one-dimensional protein structures including secondary structure, contact number, and residue-wise contact order by critical random networks method.

Kinjo, A.R. and Nishikawa, K. "Predicting secondary structures, contact numbers and residue-wise contact orders of native protein structure from amino acid sequence using critical random networks.", Biophysics, 1, 67-74 (2005).

LINPRED : 単純な線形回帰によるタンパク質の１次元構造予測（二次構造・埋も れ度・残基毎コンタクトオーダ）
Predicting the same quantities as CRNPRED, but uses straightforward multiple linear regression. Slightly less accurate than CRNPRED, but fast.

Kinjo, A.R. and Nishikawa, K. "Predicting secondary structures, contact numbers and residue-wise contact orders of native protein structure from amino acid sequence using critical random networks.", Biophysics, 1, 67-74 (2005). 　

SSThread : 3D-1D法を用いたタンパク質の二次構造予測
Prediction of protein secondary structure using threading

Masahiro Ito, Yo Matsuo and Ken Nishikawa (1997) "Prediction of protein secondary structure using the 3D-1D compatibitliy algorithm.", Comput. Appl. Biosci. 13, 415-423, 1997.

SIPPRE : アミノ酸配列からタンパク質立体構造のコンタクト数を予測
Prediction of contact numbers of protein structure from amino acid sequence.

Kinjo, A.R., Horimoto, K. and Nishikawa, K. "Predicting absolute contact numbers of native protein structure from amino acid sequence.", Proteins, 58, 158-165 (2005).

MATRAS : 立体構造比較サーバ
Protein Tertiary Structure Comparison

T.Kawabata and K.Nishikawa "Protein structure comparison using the Markov transition model of evolution". Proteins. 41, 108-122, 2000.

大腸菌関連種ゲノム比較 ( internal use only )