Presto(protein Engineering Simulator): A Vectorized Molecular Mechanics Program for Biopolymers. - Kenji Morikami; Takahisa Nakai; Akinori Kidera; Minoru Saito; Haruki Nakamura (Comput. Chem., 1992)

Peptide free-energy profile is strongly dependent on the force field: Comparison of C96 and AMBER95. - Satoshi Ono; Nobuyuki Nakajima; Junichi Higo; Haruki Nakamura (J. Comput. Chem., 2000)

Collective motions of myosin head derived from backbone molecular dynamics and combination with X-ray solution scattering data. - Junichi Higo; Yasunobu Sugimoto; Katsuzo Wakabayashi; Haruki Nakamura (J. Comput. Chem., 2001)

A method of comparing protein molecular surface based on normal vectors with attributes and its application to function identification. - Yoshikazu Kaneta; Norimasa Shoji; Takenao Ohkawa; Haruki Nakamura (Inf. Sci., 2002)

A filtering method for high-speed retrieval of similar active sites. - Tadasuke Nakagawa; Takanori Tanaka; Takenao Ohkawa; Haruki Nakamura (Inf. Sci., 2002)

Calibration of force-field dependency in free energy landscapes of peptide conformations by quantum chemical calculations. - Satoshi Ono; Masataka Kuroda; Junichi Higo; Nobuyuki Nakajima; Haruki Nakamura (J. Comput. Chem., 2002)

Information Extraction from Semi-Structured Data in the Protein Data Bank by Induction of a Data Description Pattern. - Youhei Kawaguchi; Yoshikazu Kaneta; Takenao Ohkawa; Haruki Nakamura (METMBS, 2003)

beta-Hairpins, alpha-helices, and the intermediates among the secondary structures in the energy landscape of a peptide from a distal beta-hairpin of SH3 domain. - Kazuyoshi Ikeda; Oxana V. Galzitskaya; Haruki Nakamura; Junichi Higo (J. Comput. Chem., 2003)

eF-site and PDBjViewer: database and viewer for protein functional sites. - Kengo Kinoshita; Haruki Nakamura (Bioinform., 2004)

A hybrid method of molecular dynamics and harmonic dynamics for docking of flexible ligand to flexible receptor. - Rie Tatsumi; Yoshifumi Fukunishi; Haruki Nakamura (J. Comput. Chem., 2004)

A Challenge towards Next-Generation Research Infrastructure for Advanced Life Science. - Haruki Nakamura; Susumu Date; Hideo Matsuda; Shinji Shimojo (New Gener. Comput., 2004)

Protein informatics towards integration of data grid and computing grid. - Haruki Nakamura (APBC, 2005)

PreDs: a server for predicting dsDNA-binding site on protein molecular surfaces. - Yuko Tsuchiya; Kengo Kinoshita; Haruki Nakamura (Bioinform., 2005)

PDBML: the representation of archival macromolecular structure data in XML. - John D. Westbrook; Nobutoshi Ito; Haruki Nakamura; Kim Henrick; Helen M. Berman (Bioinform., 2005)

Filtering high-throughput protein-protein interaction data using a combination of genomic features. - Ashwini Patil; Haruki Nakamura (BMC Bioinform., 2005)

GASH: An improved algorithm for maximizing the number of equivalent residues between two protein structures. - Daron M. Standley; Hiroyuki Toh; Haruki Nakamura (BMC Bioinform., 2005)

Deploying Scientific Applications to the PRAGMA Grid Testbed: Strategies and Lessons. - David Abramson 001; Amanda Lynch; Hiroshi Takemiya; Yusuke Tanimura; Susumu Date; Haruki Nakamura; Karpjoo Jeong; Suntae Hwang; Ji Zhu; Zhonghua Lu; Céline Amoreira; Kim K. Baldridge; et al. (CCGRID, 2006)

A Virtual Active Compound Produced from the Negative Image of a Ligand-binding Pocket, and its Application to in-silico Drug Screening. - Yoshifumi Fukunishi; Satoru Kubota; Chisato Kanai; Haruki Nakamura (J. Comput. Aided Mol. Des., 2006)

An Efficient in Silico Screening Method Based on the Protein-Compound Affinity Matrix and Its Application to the Design of a Focused Library for Cytochrome P450 (CYP) Ligands. - Yoshifumi Fukunishi; Shinichi Hojo; Haruki Nakamura (J. Chem. Inf. Model., 2006)

Noise Reduction Method for Molecular Interaction Energy: Application to in Silico Drug Screening and in Silico Target Protein Screening. - Yoshifumi Fukunishi; Satoru Kubota; Haruki Nakamura (J. Chem. Inf. Model., 2006)

PreBI: prediction of biological interfaces of proteins in crystals. - Yuko Tsuchiya; Kengo Kinoshita; Nobutoshi Ito; Haruki Nakamura (Nucleic Acids Res., 2006)

A Grid-Ready Clinical Database for Parkinson's Disease Research and Diagnosis. - Susumu Date; Takahito Tashiro; Kazunori Nozaki; Haruki Nakamura; Saburo Sakoda; Shinji Shimojo (CBMS, 2007)

ASH structure alignment package: Sensitivity and selectivity in domain classification. - Daron M. Standley; Hiroyuki Toh; Haruki Nakamura (BMC Bioinform., 2007)

The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. - Helen M. Berman; Kim Henrick; Haruki Nakamura; John L. Markley (Nucleic Acids Res., 2007)

eF-seek: prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape. - Kengo Kinoshita; Yoichi Murakami; Haruki Nakamura (Nucleic Acids Res., 2007)

Protein structure databases with new web services for structural biology and biomedical research. - Daron M. Standley; Akira R. Kinjo; Kengo Kinoshita; Haruki Nakamura (Briefings Bioinform., 2008)

Improvement of Protein-Compound Docking Scores by Using Amino-Acid Sequence Similarities of Proteins. - Yoshifumi Fukunishi; Haruki Nakamura (J. Chem. Inf. Model., 2008)

Remediation of the protein data bank archive. - Kim Henrick; Zukang Feng; Wolfgang Bluhm; Dimitris Dimitropoulos; Jurgen F. Doreleijers; Shuchismita Dutta; Judith L. Flippen-Anderson; John M. C. Ionides; Chisa Kamada; Eugene Krissinel; Catherine L. Lawson; John L. Markley; et al. (Nucleic Acids Res., 2008)

Protein function annotation from sequence: prediction of residues interacting with RNA. - Ruth V. Spriggs; Yoichi Murakami; Haruki Nakamura; Susan Jones (Bioinform., 2009)

A Grid-aware Access Control Mechanism in a Clinical Database for Parkinson's Disease Research and Diagnosis. - Susumu Date; Kazunori Nozaki; Haruki Nakamura; Saburo Sakoda; Shinji Shimojo (Inf. Media Technol., 2009)

Application of MDGRAPE-3, a special purpose board for molecular dynamics simulations, to periodic biomolecular systems. - Gota Kikugawa; Rossen Apostolov; Narutoshi Kamiya; Makoto Taiji; Ryutaro Himeno; Haruki Nakamura; Yasushige Yonezawa (J. Comput. Chem., 2009)

Numerical examination of the extended phase-space volume-preserving integrator by the Nosé-Hoover molecular dynamics equations. - Séverine Queyroy; Haruki Nakamura; Ikuo Fukuda (J. Comput. Chem., 2009)

Protein-Ligand Binding Free Energy Calculation by the Smooth Reaction Path Generation (SRPG) Method. - Yoshifumi Fukunishi; Daisuke Mitomo; Haruki Nakamura (J. Chem. Inf. Model., 2009)

In Silico Fragment Screening by Replica Generation (FSRG) Method for Fragment-Based Drug Design. - Yoshifumi Fukunishi; Tadaaki Mashimo; Masaya Orita; Kazuki Ohno; Haruki Nakamura (J. Chem. Inf. Model., 2009)

PDBj Mine: design and implementation of relational database interface for Protein Data Bank Japan. - Akira R. Kinjo; Reiko Yamashita; Haruki Nakamura (Database J. Biol. Databases Curation, 2010)

SeSAW: balancing sequence and structural information in protein functional mapping. - Daron M. Standley; Reiko Yamashita; Akira R. Kinjo; Hiroyuki Toh; Haruki Nakamura (Bioinform., 2010)

Electronic structures of heme a of cytochrome c oxidase in the redox states - Charge density migration to the propionate groups of heme a. - Yu Takano; Haruki Nakamura (J. Comput. Chem., 2010)

Selection of In Silico Drug Screening Results by Using Universal Active Probes (UAPs). - Yoshifumi Fukunishi; Kazuki Ohno; Masaya Orita; Haruki Nakamura (J. Chem. Inf. Model., 2010)

PiRaNhA: a server for the computational prediction of RNA-binding residues in protein sequences. - Yoichi Murakami; Ruth V. Spriggs; Haruki Nakamura; Susan Jones (Nucleic Acids Res., 2010)

Theory for trivial trajectory parallelization of multicanonical molecular dynamics and application to a polypeptide in water. - Jinzen Ikebe; Koji Umezawa; Narutoshi Kamiya; Takanori Sugihara; Yasushige Yonezawa; Yu Takano; Haruki Nakamura; Junichi Higo (J. Comput. Chem., 2011)

Definition of Drug-Likeness for Compound Affinity. - Yoshifumi Fukunishi; Haruki Nakamura (J. Chem. Inf. Model., 2011)

Selection of In Silico Drug Screening Results for G-Protein-Coupled Receptors by Using Universal Active Probes. - Mitsuhito Wada; Eiji Kanamori; Haruki Nakamura; Yoshifumi Fukunishi (J. Chem. Inf. Model., 2011)

HitPredict: a database of quality assessed protein-protein interactions in nine species. - Ashwini Patil; Kenta Nakai; Haruki Nakamura (Nucleic Acids Res., 2011)

Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format. - Akira R. Kinjo; Hirofumi Suzuki; Reiko Yamashita; Yasuyo Ikegawa; Takahiro Kudou; Reiko Igarashi; Yumiko Kengaku; Hasumi Cho; Daron M. Standley; Atsushi Nakagawa; Haruki Nakamura (Nucleic Acids Res., 2012)

Protein Experimental Information Management System (PREIMS) Based on Ontology: Development and Applications. - Junko Sato; Kouji Kozaki; Susumu Handa; Takashi Ikeda; Ryotaro Saka; Kohei Tomizuka; Yugo Nishiyama; Toshiyuki Okumura; Shinichi Hirai; Tadashi Ohno; Mamoru Ohta; Susumu Date; et al. (Inf. Media Technol., 2013)

Kotai Antibody Builder: automated high-resolution structural modeling of antibodies. - Kazuo Yamashita; Kazuyoshi Ikeda; Karlou Mar Amada; Shide Liang; Yuko Tsuchiya; Haruki Nakamura; Hiroki Shirai; Daron M. Standley (Bioinform., 2014)

The Protein Data Bank archive as an open data resource. - Helen M. Berman; Gerard J. Kleywegt; Haruki Nakamura; John L. Markley (J. Comput. Aided Mol. Des., 2014)

Prediction of Synthetic Accessibility Based on Commercially Available Compound Databases. - Yoshifumi Fukunishi; Takashi Kurosawa; Yoshiaki Mikami; Haruki Nakamura (J. Chem. Inf. Model., 2014)

3D Flexible Alignment Using 2D Maximum Common Substructure: Dependence of Prediction Accuracy on Target-Reference Chemical Similarity. - Takeshi Kawabata; Haruki Nakamura (J. Chem. Inf. Model., 2014)

A(touch)ment: a smartphone extension for instantly sharing visual and tactile experience. - Haruki Nakamura; Nobuhisa Hanamitsu; Kouta Minamizawa (AH, 2015)

Twech: a mobile platform to search and share visuo-tactile experiences. - Nobuhisa Hanamitsu; Haruki Nakamura; Masashi Nakatani; Kouta Minamizawa (SIGGRAPH Asia Mobile Graphics and Interactive Applications, 2015)

Twech: a mobile platform to search and share visuo-tactile experiences. - Nobuhisa Hanamitsu; Haruki Nakamura; Masashi Nakatani; Kouta Minamizawa (SIGGRAPH Asia Emerging Technologies, 2015)

Virtual-system-coupled adaptive umbrella sampling to compute free-energy landscape for flexible molecular docking. - Junichi Higo; Bhaskar Dasgupta; Tadaaki Mashimo; Kota Kasahara; Yoshifumi Fukunishi; Haruki Nakamura (J. Comput. Chem., 2015)

Computational Study of Drug Binding Affinity to Influenza A Neuraminidase Using Smooth Reaction Path Generation (SRPG) Method. - Hung Nguyen; Tien Tran; Yoshifumi Fukunishi; Junichi Higo; Haruki Nakamura; Ly Le (J. Chem. Inf. Model., 2015)

A Finger Sensor for Sharing Visual and Tactile Experience. - Haruki Nakamura; Nobuhisa Hanamitsu; Junichi Kanebako; Kouta Minamizawa (AsiaHaptics, 2016)

mDCC_tools: characterizing multi-modal atomic motions in molecular dynamics trajectories. - Kota Kasahara; Neetha Mohan; Ikuo Fukuda; Haruki Nakamura (Bioinform., 2016)

Omokage search: shape similarity search service for biomolecular structures in both the PDB and EMDB. - Hirofumi Suzuki; Takeshi Kawabata; Haruki Nakamura (Bioinform., 2016)

Publication of nuclear magnetic resonance experimental data with semantic web technology and the application thereof to biomedical research of proteins. - Masashi Yokochi; Naohiro Kobayashi; Eldon L. Ulrich; Akira R. Kinjo; Takeshi Iwata; Yannis E. Ioannidis; Miron Livny; John L. Markley; Haruki Nakamura; Chojiro Kojima; Toshimichi Fujiwara (J. Biomed. Semant., 2016)

Variation of free-energy landscape of the p53 C-terminal domain induced by acetylation: Enhanced conformational sampling. - Shinji Iida; Tadaaki Mashimo; Takashi Kurosawa; Hironobu Hojo; Hiroya Muta; Yuji Goto; Yoshifumi Fukunishi; Haruki Nakamura; Junichi Higo (J. Comput. Chem., 2016)

Development of massive multilevel molecular dynamics simulation program, platypus (PLATform for dYnamic protein unified simulation), for the elucidation of protein functions. - Yu Takano; Kazuto Nakata; Yasushige Yonezawa; Haruki Nakamura (J. Comput. Chem., 2016)

Molmil: a molecular viewer for the PDB and beyond. - Gert-Jan Bekker; Haruki Nakamura; Akira R. Kinjo (J. Cheminformatics, 2016)

Model Building of Antibody-Antigen Complex Structures Using GBSA Scores. - Noriko Shimba; Narutoshi Kamiya; Haruki Nakamura (J. Chem. Inf. Model., 2016)

Web-based Molecular Graphics (NII Shonan Meeting 2016-12). - Andrea Schafferhans; Seán I. O'Donoghue; Haruki Nakamura (NII Shonan Meet. Rep., 2016)

HaptI/O: Physical Node for the Internet of Haptics. - Satoshi Matsuzono; Haruki Nakamura; Daiya Kato; Roshan Lalintha Peiris; Kouta Minamizawa (UIST (Adjunct Volume), 2017)

Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures. - Akira R. Kinjo; Gert-Jan Bekker; Hirofumi Suzuki; Yuko Tsuchiya; Takeshi Kawabata; Yasuyo Ikegawa; Haruki Nakamura (Nucleic Acids Res., 2017)

HaptI/O: Physical I/O Node over the Internet. - Satoshi Matsuzono; Haruki Nakamura; Daiya Kato; Roshan Lalintha Peiris; Kouta Minamizawa (EuroHaptics (2), 2018)

Construction of Haptic Experience Sharing Platform. - Haruki Nakamura; Daiya Kato; Roshan Lalintha Peiris; Kouta Minamizawa; Yutaka Kamamoto; Junji Watanabe (UbiComp/ISWC Adjunct, 2018)

Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data. - Jasmine Young; John D. Westbrook; Zukang Feng; Ezra Peisach; Irina Persikova; Raul Sala; Sanchayita Sen; John M. Berrisford; Jawahar Swaminathan; Thomas J. Oldfield; Aleksandras Gutmanas; Reiko Igarashi; et al. (Database J. Biol. Databases Curation, 2018)

Molecular dynamics coupled with a virtual system for effective conformational sampling. - Tomonori Hayami; Kota Kasahara; Haruki Nakamura; Junichi Higo (J. Comput. Chem., 2018)

Density functional study of porphyrin distortion effects on redox potential of heme. - Yasuhiro Imada; Haruki Nakamura; Yu Takano (J. Comput. Chem., 2018)

Multidimensional virtual-system coupled canonical molecular dynamics to compute free-energy landscapes of peptide multimer assembly. - Tomonori Hayami; Junichi Higo; Haruki Nakamura; Kota Kasahara (J. Comput. Chem., 2019)

Hydrogen bond donors and acceptors are generally depolarized in α-helices as revealed by a molecular tailoring approach. - Hiroko X. Kondo; Ayumi Kusaka; Colin K. Kitakawa; Jinta Onari; Shusuke Yamanaka; Haruki Nakamura; Yu Takano (J. Comput. Chem., 2019)

Molecular Interaction Mechanism of a 14-3-3 Protein with a Phosphorylated Peptide Elucidated by Enhanced Conformational Sampling. - Junichi Higo; Takeshi Kawabata; Ayumi Kusaka; Kota Kasahara; Narutoshi Kamiya; Ikuo Fukuda; Kentaro Mori; Yutaka Hata; Yoshifumi Fukunishi; Haruki Nakamura (J. Chem. Inf. Model., 2020)

Phenology analysis for trait prediction using UAVs in a MAGIC rice population with different transplanting protocols. - Shoji Taniguchi; Toshihiro Sakamoto; Haruki Nakamura; Yasunori Nonoue; Di Guan; Akari Fukuda; Hirofumi Fukuda; Kaede C. Wada; Takuro Ishii; Jun-Ichi Yonemaru; Daisuke Ogawa (Frontiers Artif. Intell., 2024)