Bunkyō-ku, Japan
Bunkyō-ku, Japan

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Motono C.,Japan National Institute of Advanced Industrial Science and Technology | Motono C.,Japan Science and Technology Agency | Nakata J.,Japan National Institute of Advanced Industrial Science and Technology | Nakata J.,Japan Science and Technology Agency | And 35 more authors.
Nucleic Acids Research | Year: 2011

Most proteins from higher organisms are known to be multi-domain proteins and contain substantial numbers of intrinsically disordered (ID) regions. To analyse such protein sequences, those from human for instance, we developed a special proteinstructure-prediction pipeline and accumulated the products in the Structure Atlas of Human Genome (SAHG) database at http://bird.cbrc.jp/sahg. With the pipeline, human proteins were examined by local alignment methods (BLAST, PSI-BLAST and Smith-Waterman profile-profile alignment), global-local alignment methods (FORTE) and prediction tools for ID regions (POODLE-S) and homology modeling (MODELLER). Conformational changes of protein models upon ligand-binding were predicted by simultaneous modeling using templates of apo and holo forms. When there were no suitable templates for holo forms and the apo models were accurate, we prepared holo models using prediction methods for ligand-binding (eF-seek) and conformational change (the elastic network model and the linear response theory). Models are displayed as animated images. As of July 2010, SAHG contains 42 581 protein-domain models in approximately 24 900 unique human protein sequences from the RefSeq database. Annotation of models with functional information and links to other databases such as EzCatDB, InterPro or HPRD are also provided to facilitate understanding the protein structurefunction relationships.© The Author(s) 2010.

Yamamoto S.,Japan Science and Technology Agency | Sakai N.,Japan Science and Technology Agency | Nakamura H.,Information and Mathematical Science Laboratory Inc. | Fukagawa H.,INTEC Inc. | And 2 more authors.
Database | Year: 2011

The Integrating Network Objects with Hierarchies (INOH) database is a highly structured, manually curated database of signal transduction pathways including Mammalia, Xenopus laevis, Drosophila melanogaster, Caenorhabditis elegans and canonical. Since most pathway knowledge resides in scientific articles, the database focuses on curating and encoding textual knowledge into a machine-processable form. We use a hierarchical pathway representation model with a compound graph, and every pathway component in the INOH database is annotated by a set of uniquely developed ontologies. Finally, we developed the Similarity Search using the combination of a compound graph and hierarchical ontologies. The INOH database is to be a good resource for many users who want to analyze a large protein network. INOH ontologies and 73 signal transduction and 29 metabolic pathway diagrams (including over 6155 interactions and 3395 protein entities) are freely available in INOH XML and BioPAX formats. © The Author(s) 2011.

Hamada M.,University of Tokyo | Hamada M.,Japan National Institute of Advanced Industrial Science and Technology | Yamada K.,Information and Mathematical Science Laboratory Inc. | Sato K.,University of Tokyo | And 3 more authors.
Nucleic Acids Research | Year: 2011

Although secondary structure predictions of an individual RNA sequence have been widely used in a number of sequence analyses of RNAs, accuracy is still limited. Recently, we proposed a method (called 'CentroidHomfold'), which includes information about homologous sequences into the prediction of the secondary structure of the target sequence, and showed that it substantially improved the performance of secondary structure predictions. CentroidHomfold, however, forces users to prepare homologous sequences of the target sequence. We have developed a Web application (CentroidHomfold-LAST) that predicts the secondary structure of the target sequence using automatically collected homologous sequences. LAST, which is a fast and sensitive local aligner, and CentroidHomfold are employed in the Web application. Computational experiments with a commonly-used data set indicated that CentroidHomfold-LAST substantially outperformed conventional secondary structure predictions including CentroidFold and RNAfold. © 2011 The Author(s).

Suwa M.,Japan National Institute of Advanced Industrial Science and Technology | Sugihara M.,Japan National Institute of Advanced Industrial Science and Technology | Ono Y.,Japan National Institute of Advanced Industrial Science and Technology | Ono Y.,Information and Mathematical Science Laboratory Inc
Pharmaceuticals | Year: 2011

An understanding of the functional mechanisms of G-protein-coupled receptors (GPCRs) is very important for GPCR-related drug design. We have developed an integrated GPCR database (SEVENS http://sevens.cbrc.jp/) that includes 64,090 reliable GPCR genes comprehensively identified from 56 eukaryote genome sequences, and overviewed the sequences and structure spaces of the GPCRs. In vertebrates, the number of receptors for biological amines, peptides, etc. is conserved in most species, whereas the number of chemosensory receptors for odorant, pheromone, etc. significantly differs among species. The latter receptors tend to be single exon type or a few exon type and show a high ratio in the numbers of GPCRs, whereas some families, such as Class B and Class C receptors, have long lengths due to the presence of many exons. Statistical analyses of amino acid residues reveal that most of the conserved residues in Class A GPCRs are found in the cytoplasmic half regions of transmembrane (TM) helices, while residues characteristic to each subfamily found on the extracellular half regions. The 69 of Protein Data Bank (PDB) entries of complete or fragmentary structures could be mapped on the TM/loop regions of Class A GPCRs covering 14 subfamilies. © 2011 by the authors; licensee MDPI, Basel, Switzerland.

Azuma H.,Information and Mathematical Science Laboratory Inc. | Ban M.,Ochanomizu University
Journal of Modern Optics | Year: 2010

In this paper, we show a direct method of deriving the Peres-Horodecki criterion for the two-qubit states from the Hill-Wootters formula for the entanglement of formation. Although the Peres-Horodecki criterion and the Hill-Wootters formula are established results in the field of quantum information theory, they are proved independently and connections between them are not discussed precisely. In this paper, we clarify these connections. First, we replace the original Peres-Horodecki criterion with an equivalent statement found by Augusiak et al. [Augusiak, R.; Demianowicz, M.; Horodecki, M.; Horodecki, R. Rev. Mod. Phys. 2009, 81, 865-942]. Second, we obtain an analytical form of the concurrence of an arbitrary two-qubit state , using Ferrari's method to solve a quartic equation for eigenvalues ρρ̃. Finally, with the above preparations, we accomplish the direct derivation of the Peres-Horodecki criterion from the Hill-Wootters formula. © 2010 Taylor & Francis.

Azuma H.,Information and Mathematical Science Laboratory Inc.
International Journal of Modern Physics C | Year: 2010

In this paper, we give an analytical treatment to study the behavior of the collapse and the revival of the Rabi oscillations in the JaynesCummings model (JCM). The JCM is an exactly soluble quantum mechanical model, which describes the interaction between a two-level atom and a single cavity mode of the electromagnetic field. If we prepare the atom in the ground state and the cavity mode in a coherent state initially, the JCM causes the collapse and the revival of the Rabi oscillations many times in a complicated pattern in its time-evolution. In this phenomenon, the atomic population inversion is described with an intractable infinite series. (When the electromagnetic field is resonant with the atom, the nth term of this infinite series is given by a trigonometric function for $\sqrt{n} t$, where t is a variable of the time.) According to Klimov and Chumakov's method, using the AbelPlana formula, we rewrite this infinite series as a sum of two integrals. We examine the physical meanings of these two integrals and find that the first one represents the initial collapse (the semi-classical limit) and the second one represents the revival (the quantum correction) in the JCM. Furthermore, we evaluate the first- and second-order perturbations for the time-evolution of the JCM with an initial thermal coherent state for the cavity mode at low temperature, and write down their correction terms as sums of integrals by making use of the AbelPlana formula. © 2010 World Scientific Publishing Company.