Parallelization of Space Plasma Particle Simulation. - Yutaka Akiyama; Kiyotaka Misoo; Yoshiharu Omura; Hiroshi Matsumoto; Minoru Saito; Tamotsu Noguchi; Kentaro Onizuka; Makoto Ando (ISHPC, 1997)

Parallel PDB Data Retriever "PDB Diving Booster". - Kentaro Onizuka; Tamotsu Noguchi; Minoru Saito; Yutaka Akiyama (ISHPC, 1997)

PDB-REPRDB: A Database of Representative Protein Chains in PDB (Protein Data Bank). - Tamotsu Noguchi; Kentaro Onizuka; Yutaka Akiyama; Minoru Saito (ISMB, 1997)

Biological- and Chemical- Parallel Applications on a PC Cluster. - Yutaka Akiyama; Kentaro Onizuka; Tamotsu Noguchi; Makoto Ando (ISHPC, 1999)

ESCAPE: Parallel Tree Search System for Conformational Analysis of Peptides. - Makoto Ando; Yutaka Akiyama; Kentaro Onizuka; Tamotsu Noguchi (PDPTA, 1999)

Quick selection of representative protein chain sets based on customizable requirements. - Tamotsu Noguchi; Kentaro Onizuka; Makoto Ando; Hideo Matsuda; Yutaka Akiyama (Bioinform., 2000)

PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB). - Tamotsu Noguchi; Hideo Matsuda; Yutaka Akiyama (Nucleic Acids Res., 2001)

Using Data Compression for Multidimensional Distribution Analysis. - Kentaro Onizuka; Tamotsu Noguchi; Yutaka Akiyama; Hideo Matsuda (IEEE Intell. Syst., 2002)

PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB) in 2003. - Tamotsu Noguchi; Yutaka Akiyama (Nucleic Acids Res., 2003)

Feature Selection Based on Physicochemical Properties of Redefined N-term Region and C-term Regions for Predicting Disorder. - Kana Shimizu; Yoichi Muraoka; Shuichi Hirose; Tamotsu Noguchi (CIBCB, 2005)

Optimization and evaluation of parallel molecular dynamics simulation on blue gene/L. - Masakazu Sekijima; Junta Doi; Tamotsu Noguchi; Yutaka Akiyama; Shigenori Shimizu (Parallel and Distributed Computing and Networks, 2007)

Development of Molecular Dynamics Simulation Based Flexible Docking System. - Sachi Kimura; Masakazu Sekijima; Masami Takata; Tamotsu Noguchi; Kazuki Joe (PDPTA, 2007)

Development of an SVM based Prediction System for Metalbinding Sites in Protein. - Masami Nakazawa; Masami Takata; Kiyonobu Yokota; Tamotsu Noguchi; Masakazu Sekijima; Kazuki Joe (PDPTA, 2007)

POODLE-L: a two-level SVM prediction system for reliably predicting long disordered regions. - Shuichi Hirose; Kana Shimizu; Satoru Kanai; Yutaka Kuroda; Tamotsu Noguchi (Bioinform., 2007)

POODLE-S: web application for predicting protein disorder by using physicochemical features and reduced amino acid set of a position-specific scoring matrix. - Kana Shimizu; Shuichi Hirose; Tamotsu Noguchi (Bioinform., 2007)

Predicting mostly disordered proteins by using structure-unknown protein data. - Kana Shimizu; Yoichi Muraoka; Shuichi Hirose; Kentaro Tomii; Tamotsu Noguchi (BMC Bioinform., 2007)

Large-Scale Computing for Protein-Protein Binding Free Energy Calculation. - Junichi Ikeda; Kazuki Ohno; Sayaka Akioka; Masaya Orita; Yoichi Muraoka; Tamotsu Noguchi; Masakazu Sekijima (PDPTA, 2008)

Free Energy Landscape Analysis System Based on Parallel Molecular Dynamics Simulation. - Masakazu Sekijima; Junta Doi; Shinya Honda; Tamotsu Noguchi; Shigenori Shimizu; Yutaka Akiyama (Inf. Media Technol., 2008)

The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. - Toshiaki Katayama; Kazuharu Arakawa; Mitsuteru Nakao; Keiichiro Ono; Kiyoko F. Aoki-Kinoshita; Yasunori Yamamoto; Atsuko Yamaguchi; Shuichi Kawashima; Hong-Woo Chun; Jan Aerts; Bruno Aranda; Lord H. Barboza; et al. (J. Biomed. Semant., 2010)

POODLE-I: Disordered Region Prediction by Integrating POODLE Series and Structural Information Predictors Based on a Workflow Approach. - Shuichi Hirose; Kana Shimizu; Tamotsu Noguchi (Silico Biol., 2010)

SAHG, a comprehensive database of predicted structures of all human proteins. - Chie Motono; Junichi Nakata; Ryotaro Koike; Kana Shimizu; Matsuyuki Shirota; Takayuki Amemiya; Kentaro Tomii; Nozomi Nagano; Naofumi Sakaya; Kiyotaka Misoo; Miwa Sato; Akinori Kidera; et al. (Nucleic Acids Res., 2011)

MFSPSSMpred: identifying short disorder-to-order binding regions in disordered proteins based on contextual local evolutionary conservation. - Chun Fang; Tamotsu Noguchi; Daisuke Tominaga; Hayato Yamana (BMC Bioinform., 2013)

SCPSSMpred: A General Sequence-based Method for Ligand-binding Site Prediction. - Chun Fang; Tamotsu Noguchi; Hayato Yamana (Inf. Media Technol., 2013)

Simplified sequence-based method for ATP-binding prediction using contextual local evolutionary conservation. - Chun Fang; Tamotsu Noguchi; Hayato Yamana (Algorithms Mol. Biol., 2014)

Analysis of evolutionary conservation patterns and their influence on identifying protein functional sites. - Chun Fang; Tamotsu Noguchi; Hayato Yamana (J. Bioinform. Comput. Biol., 2014)

Condensing position-specific scoring matrixs by the Kidera factors for ligand-binding site prediction. - Chun Fang; Tamotsu Noguchi; Hayato Yamana (Int. J. Data Min. Bioinform., 2015)

Identifying Protein Short Linear Motifs by Position-Specific Scoring Matrix. - Chun Fang; Tamotsu Noguchi; Hayato Yamana; Fuzhen Sun (ICSI (2), 2016)

A Privacy-Preserving Query System using Fully Homomorphic Encryption with Real-World Implementation for Medicine-Side Effect Search. - Yusheng Jiang; Tamotsu Noguchi; Nobuyuki Kanno; Yoshiko Yasumura; Takuya Suzuki; Yu Ishimaki; Hayato Yamana (iiWAS, 2019)