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Matsuoka Y.,The Systems Biology Institute | Matsuoka Y.,A+ Network | Ghosh S.,The Systems Biology Institute | Kikuchi N.,Mitsui Knowledge Industry Co. | And 3 more authors.
Bioinformatics | Year: 2010

Summary: Payao is a community-based, collaborative web service platform for gene-regulatory and biochemical pathway model curation. The system combines Web 2.0 technologies and online model visualization functions to enable a collaborative community to annotate and curate biological models. Payao reads the models in Systems Biology Markup Language format, displays them with CellDesigner, a process diagram editor, which complies with the Systems Biology Graphical Notation, and provides an interface for model enrichment (adding tags and comments to the models) for the access-controlled community members. Availability and implementation: Freely available for model curation service at http://www.payaologue.org. Web site implemented in Seaser Framework 2.0 with S2Flex2, MySQL 5.0 and Tomcat 5.5, with all major browsers supported. Contact: kitano@sbi.jp. © The Author 2010. Published by Oxford University Press.

Sato M.,Yokohama City University | Sato M.,Japan National Institute of Advanced Industrial Science and Technology | Sato M.,Mitsui Knowledge Industry Co. | Hirokawa T.,Japan National Institute of Advanced Industrial Science and Technology
Journal of Chemical Information and Modeling | Year: 2014

G-protein-coupled receptors (GPCRs) are a pharmaceutically important protein family because they mediate numerous physiological functions. The crystal structures of several GPCR subtypes have been determined recently, encouraging efforts to apply structure-based virtual screening (SBVS) along with ligand-based virtual screening (LBVS) to improve the hit rate of active ligands from large chemical libraries. Three-dimensional models are also necessary for GPCR targets whose structures are unknown. Current challenges include the selection of structural templates from available structurally known GPCRs to use for accurate modeling and understanding the diversity of sites recognizing distinct ligands. We have developed and validated an extended template-based modeling and evaluation method for SBVS. Models were generated using a fragmental template procedure in addition to typical template-based modeling methods. The reliability of the models was evaluated using a virtual screening test with known active ligands and decoys and the consensus of the binding mode using the protein-ligand interaction fingerprint (PLIF) derived from the results of docking simulations. This novel workflow was applied to three targets with known structures (human dopamine receptor 3, human histamine H1 receptor, and human delta opioid receptor) and to a target with an unknown structure (human serotonin 2A receptor). In each case, model structures having high ligand selectivity with consensus binding mode were generated. (Figure Presented) © 2014 American Chemical Society.

Shiota T.,Monash University | Shiota T.,Nagoya University | Imai K.,Japan National Institute of Advanced Industrial Science and Technology | Qiu J.,Albert Ludwigs University of Freiburg | And 19 more authors.
Science | Year: 2015

Mitochondria fulfill central functions in cellular energetics, metabolism, and signaling.The outer membrane translocator complex (the TOM complex) imports most mitochondrial proteins, but its architecture is unknown. Using a cross-linking approach, we mapped the active translocator down to single amino acid residues, revealing different transport paths for preproteins through the Tom40 channel. An N-terminal segment of Tom40 passes from the cytosol through the channel to recruit chaperones from the intermembrane space that guide the transfer of hydrophobic preproteins. The translocator contains three Tom40 β-barrel channels sandwiched between a central α-helical Tom22 receptor cluster and external regulatory Tom proteins. The preprotein-translocating trimeric complex exchanges with a dimeric isoform to assemble new TOM complexes. Dynamic coupling of a-helical receptors, β-barrel channels, and chaperones generates a versatile machinery that transports about 1000 different proteins.

Mitsui Knowledge Industry Co. | Date: 2013-11-29

Computer software for scientific and medical research and analysis. Providing temporary use of online non-downloadable computer software for scientific and medical research and analysis; Design, development, maintenance, update and computer network configuration services of computer software for scientific and medical research and analysis; Design, development and maintenance of computer systems for scientific and medical research and analysis.

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.

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