[18] Biomolecular Structure Databases.

Daisuke Kihara.

Genome Function Research Handbook, Chapter 2. pp. 73-81. Yodosha Publishers, Tokyo, Japan. (2004).

[17] Development and large scale benchmark testing of the PROSPECTOR 3.0 threading algorithm.

Jeffrey Skolnick, Daisuke Kihara and Yang Zhang.

Proteins: Structure, Funct. Bioinformatics 56:502-518. (2004)

[16] Microbial genomes have over 72% structure assignment by the threading algorithm

PROSPECTOR_Q.

Daisuke Kihara and Jeffrey Skolnick.

Proteins: Structure, Funct. Bioinformatics 55: 464-473 (2004)

[15] The PDB is a covering set of small protein structures.

Daisuke Kihara and Jeffrey Skolnick.

J. Mol. Biol. 334: 793-802 (2003)

[14] TOUCHSTONE: a unified approach to protein structure prediction.

Jeffrey Skolnick, Yang Zhang, Adrian Arakaki, Andrzej Kolinski, Michael Boniecki,

Andras Szilagyi and Daisuke Kihara.

Proteins: Structure, Funct. Genet. 53: Suppl.6: 469-479 (2003)

[13] TOUCHSTONEX: Protein Structure Prediction Using Sparse NMR Data.

Wei Li, Yang Zhang, Daisuke Kihara, Yuanpeng J. Huang, Deyou Zheng,

Gaetano T. Montelione, Andrzej Kolinski, and Jeffrey Skolnick

Proteins: Structure, Funct. Genet. 53: 290-306 (2003)

[12] Local Energy Landscape Flattening: Parallel Hyperbolic Monte Carlo Sampling

of Protein Folding.

Yang, Zhang, Daisuke Kihara and Jeffrey Skolnick

Proteins: Structure, Funct. Genet. 48: 192-201 (2002)

[11] Ab initio Protein Structure Prediction on a Genomic Scale: Application to the

Mycoplasma genitalium Genome.

Daisuke Kihara, Yang Zhang, Hui Lu, Andrzej Kolinski and Jeffrey Skolnick

Proc. Natl. Acad. Sci. USA, 99: 5993-5998 (2002)

[10] Ab initio Protein Structure Prediction via a Combination of Threading, Lattice

Folding, Clustering, and Structure Refinement.

Jeffrey Skolnick, Andrzej Kolinski, Daisuke Kihara, Marcos Betancourt, Piotr

Rotkiewicz and Michael Boniecki

Proteins: Structure, Funct. Genet. 45 (Suppl 5): 149-156 (2001)

[9] Genome Databases on the Internet.

Daisuke Kihara

Tanpakushitsu Kakusan Koso (Protein, Nucleic Acid and Enzyme)

46 (16 Suppl): 2639-2645 (2001)

[8] Prediction of Membrane Proteins in Post-Genomic Era.

Daisuke Kihara and Minoru Kanehisa

Recent Res. Developments in Protein Engng. 1: 179-196 (2001)

[7] TOUCHSTONE: An ab initio Protein Structure Prediction Method that Uses

Threading-based Tertiary Restraints.

Daisuke Kihara, Hui Lu, Andrzej Kolinski and Jeffrey Skolnick

Proc. Natl. Acad. Sci. USA 98: 10125-10130 (2001)

[6] Generalized Comparative Modeling (GENCOMP): A Combination of Sequence

Comparison, Threading, and Lattice Modeling for Protein Structure Prediction

and Refinement.

Andrzej Kolinski, Marcos Betancourt, Daisuke Kihara, Piotr Rotkiewicz and Jeffrey Skolnick

Proteins: Structure, Funct. Genet. 44: 133-149 (2001)

[5] Defrosting the Frozen Approximation: PROSPECTOR – A New Approach to

Threading.

Jeffrey Skolnick and Daisuke Kihara

Proteins: Structure, Funct. Genet. 42: 319-331 (2001)

[4] Tandem Cluster of Membrane Proteins in Complete Genome Sequences.

Daisuke Kihara and Minoru Kanehisa

Genome Res. 10: 731-743 (2000)

[3] The Genome Projects and Bioinformatics.

Daisuke Kihara and Minoru Kanehisa.

Iwanami Kouza (Iwanami Lecture Series): Gendai Igaku no Kiso (The Basis of

Modern Medical Science), vol.1, Chap.11, pp: 215-235, Iwanami Shoten

Publishers, Tokyo Japan (1998)

[2] Prediction of Membrane Proteins Based on Classification of Transmembrane

Segments.

Daisuke Kihara, Toshio Shimizu and Minoru Kanehisa

Protein Engng., 11: 961-970 (1998)

[1] Internet Resources for Genome Research.

Daisuke Kihara, Minoru Kanehisa and Toshihisa Takagi.

Tanpakushitsu Kakusan Koso (Protein, Nucleic Acid and Enzyme),

42(17 Suppl): 3090-3099 (1997)