研究者詳細 - 森田　瑞樹

論文 - 森田　瑞樹

分割表示 49 件中 41 - 49 件目／全件表示 >>

Influenza patients are invisible in the web: Traditional model still improves the state-of-the-art web based influenza surveillance

Eiji Aramaki, Sachiko Maskawa, Mizuki Morita

AAAI Spring Symposium - Technical Report SS-12-05 5 - 8 2012年

掲載種別：研究論文（国際会議プロシーディングス）

Although web-based information extraction systems draw much attention, most of such systems assume that the web directly reflects the real world. For instance, Google flu trend, which is one of the-state-of-the-art influenza surveillance systems, relies on the basic idea that the amount of the influenza related search queries directly correlates with the number of the influenza patients. However, the real patients suffering from influenza symptoms are invisible in the web, because they do not use Internet. Considering this gap, this paper employs an infectious model, assuming that a potential patient utilizes Internet at the first sign of flu. The proposed model improves two types of the state-of-the-art systems, Google based system (from 0.837 correlation to 0.928) and Twitter based system (from 0.898 correlation to 0.918). This study demonstrated that a simple model could easily improve the web-based surveillance. Copyright © 2012, Association for the Advancement of Artificial Intelligence. All rights reserved.

Scopus

researchmap

Lipid recognition propensities of amino acids in membrane proteins from atomic resolution data 査読

Mizuki Morita, AVSK M. Katta, Shandar Ahmad, Takaharu Mori, Yuji Sugita, Kenji Mizuguchi

BMC Biophysics 4 ( 1 ) 21 2011年12月

記述言語：英語掲載種別：研究論文（学術雑誌）

Background: Protein-lipid interactions play essential roles in the conformational stability and biological functions of membrane proteins. However, few of the previous computational studies have taken into account the atomic details of protein-lipid interactions explicitly.Results: To gain an insight into the molecular mechanisms of the recognition of lipid molecules by membrane proteins, we investigated amino acid propensities in membrane proteins for interacting with the head and tail groups of lipid molecules. We observed a common pattern of lipid tail-amino acid interactions in two different data sources, crystal structures and molecular dynamics simulations. These interactions are largely explained by general lipophilicity, whereas the preferences for lipid head groups vary among individual proteins. We also found that membrane and water-soluble proteins utilize essentially an identical set of amino acids for interacting with lipid head and tail groups.Conclusions: We showed that the lipophilicity of amino acid residues determines the amino acid preferences for lipid tail groups in both membrane and water-soluble proteins, suggesting that tightly-bound lipid molecules and lipids in the annular shell interact with membrane proteins in a similar manner. In contrast, interactions between lipid head groups and amino acids showed a more variable pattern, apparently constrained by each protein's specific molecular function. © 2011 Morita et al
licensee BioMed Central Ltd.

DOI： 10.1186/2046-1682-4-21

Scopus

PubMed

researchmap

Twitter Catches The Flu: Detecting Influenza Epidemics using Twitter Streams 査読

Eiji Aramaki, Sachiko Maskawa, Mizuki Morita

Proceedings of the 2011 Conference on Empirical Methods in Natural Language Processing (EMNLP 2011) 1568 - 1576 2011年7月

BUDDY-system: A web site for constructing a dataset of protein pairs between ligand-bound and unbound states 査読

Mizuki Morita, Tohru Terada, Shugo Nakamura, Kentaro Shimizu

BMC Research Notes 4 143 2011年

記述言語：英語掲載種別：研究論文（学術雑誌）

Background: Elucidating molecular recognition by proteins, such as in enzyme-substrate and receptor-ligand interactions, is a key to understanding biological phenomena. To delineate these protein interactions, it is important to perform structural bioinformatics studies relevant to molecular recognition. Such studies require a dataset of protein structure pairs between ligand-bound and unbound states. In many studies, the same well-designed and high-quality dataset has been used repeatedly, which has spurred the development of subsequent relevant research. Using previously constructed datasets, researchers are able to fairly compare obtained results with those of other studies
in addition, much effort and time is saved. Therefore, it is important to construct a refined dataset that will appeal to many researchers. However, constructing such datasets is not a trivial task. Findings. We have developed the BUDDY-system, a web site designed to support the building of a dataset comprising pairs of protein structures between ligand-bound and unbound states, which are widely used in various areas associated with molecular recognition. In addition to constructing a dataset, the BUDDY-system also allows the user to search for ligand-bound protein structures by its unbound state or by its ligand
and to search for ligands by a particular receptor protein. Conclusions: The BUDDY-system receives input from the user as a single entry or a dataset consisting of a list of ligand-bound state protein structures, unbound state protein structures, or ligands and returns to the user a list of protein structure pairs between the ligand-bound and the corresponding unbound states. This web site is designed for researchers who are involved not only in structural bioinformatics but also in experimental studies. The BUDDY-system is freely available on the web. © 2011 Morita et al
licensee BioMed Central Ltd.

DOI： 10.1186/1756-0500-4-143

Scopus

PubMed

researchmap

Prediction of carbohydrate-binding proteins from sequences using support vector machines 査読

Seizi Someya, Masanori Kakuta, Mizuki Morita, Kazuya Sumikoshi, Wei Cao, Zhenyi Ge, Osamu Hirose, Shugo Nakamura, Tohru Terada, Kentaro Shimizu

Advances in Bioinformatics 2010 289301 2010年

記述言語：英語掲載種別：研究論文（学術雑誌）

Carbohydrate-binding proteins are proteins that can interact with sugar chains but do not modify them. They are involved in many physiological functions, and we have developed a method for predicting them from their amino acid sequences. Our method is based on support vector machines (SVMs). We first clarified the definition of carbohydrate-binding proteins and then constructed positive and negative datasets with which the SVMs were trained. By applying the leave-one-out test to these datasets, our method delivered 0.92 of the area under the receiver operating characteristic (ROC) curve. We also examined two amino acid grouping methods that enable effective learning of sequence patterns and evaluated the performance of these methods. When we applied our method in combination with the homology-based prediction method to the annotated human genome database, H-invDB, we found that the true positive rate of prediction was improved. © 2010 Seizi Someya et al.

DOI： 10.1155/2010/289301

Scopus

PubMed

researchmap

Structural bases of GM1 gangliosidosis and Morquio B disease 査読国際誌

Mizuki Morita, Seiji Saito, Kazuyoshi Ikeda, Kazuki Ohno, Kanako Sugawara, Toshihiro Suzuki, Tadayasu Togawa, Hitoshi Sakuraba

Journal of Human Genetics 54 ( 9 ) 510 - 515 2009年9月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：Nature Publishing Group

Allelic mutations of the lysosomal beta-galactosidase gene cause heterogeneous clinical phenotypes, such as GM1 gangliosidosis and Morquio B disease, the former being further classified into three variants, namely infantile, juvenile and adult forms; and heterogeneous biochemical phenotypes were shown in these forms. We tried to elucidate the bases of these diseases from a structural viewpoint. We first constructed a three-dimensional structural model of human beta-galactosidase by means of homology modeling. The human beta-galactosidase consists of three domains, such as, a TIM barrel fold domain, which functions as a catalytic domain, and two galactose-binding domain-like fold domains. We then constructed structural models of representative mutant beta-galactosidase proteins (G123R, R201C, I51T and Y83H) and predicted the structural change associated with each phenotype by calculating the number of affected atoms, determining the root-mean-square deviation and the solvent-accessible surface area, and by color imaging. The results show that there is a good correlation between the structural changes caused by amino-acid substitutions in the beta-galactosidase molecule, as well as biochemical and clinical phenotypes in these representative cases. Protein structural study is useful for elucidating the bases of these diseases. Journal Human Genetics (2009) 54, 510-515; doi:10.1038/jhg.2009.70; published online 31 July 2009

DOI： 10.1038/jhg.2009.70

Web of Science

PubMed

researchmap

Added mass effect on immobilizations of proteins on a 27 MHz quartz crystal microbalance in aqueous solution 査読

Hiroyuki Furusawa, Tomomitsu Ozeki, Mizuki Morita, Yoshio Okahata

Analytical Chemistry 81 ( 6 ) 2268 - 2273 2009年3月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：6

During the immobilization process of proteins onto an Au-surface of a 27 MHz quartz crystal microbalance (QCM) in aqueous solutions, apparent large frequency changes (ΔFwater) were observed compared with those in the air phase (ΔFair) due to the interaction with surrounding water of proteins. On the basis of an energy-transfer model for the QCM, the apparent added mass in the aqueous solution [(-ΔF water)/(-ΔFair) - 1] could be explained by frictional forces at the interface of proteins with aqueous solutions. When [(-ΔFwater)/(-ΔFair) -1] values for various proteins were plotted against values relating to the friction (antimobility), such as values of the molecular weight divided by the sedimentation coefficient (Mw/s), the inverse of the diffusion coefficient (1/D), and the volume divided by the surface area (volume/surface area) apparent radius) of proteins, there were good linear correlations. Thus, observations of the larger ΔF water than ΔFair for protein immobilizations on the QCM can be simply explained by the friction effect at the interface between proteins and the aqueous solution. Thus, QCM would be a mass sensor based on mechanical oscillation motion even in aqueous solutions.

DOI： 10.1021/ac802412t

Scopus

PubMed

researchmap

Highly accurate method for ligand-binding site prediction in unbound state (apo) protein structures 査読国際誌

Mizuki Morita, Shugo Nakamura, Kentaro Shimizu

Proteins: Structure, Function, and Bioinformatics 73 ( 2 ) 468 - 479 2008年11月

担当区分：筆頭著者記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：Wiley-Liss

This article describes a new method for predicting ligand-binding sites of proteins. The method involves calculating the van der Waals interaction energy between a protein and probes placed on the protein surface, and then clustering the probes with attractive interaction to find the energetically most favorable locus. In 80% (28/35) of the test cases, the ligand-binding site was successfully predicted on a ligand-bound protein structure, and in 77% (27/35) was successfully predicted on an unbound structure. Our method was used to successfully predict ligand-binding sites unaffected by induced-fit as long as its scales were not very large, and it contributed to a significant improvement in prediction with unbound state protein structures. This represents a significant advance over conventional methods in detecting ligand-binding sites on uncharacterized proteins. Moreover, our method can predict ligand-binding sites with a narrower locus than those achieved using conventional methods.

DOI： 10.1002/prot.22067

Web of Science

PubMed

researchmap

Hydration and energy dissipation measurements of biomolecules on a piezoelectric quartz oscillator by admittance analyses 査読国際誌

Tomomitsu Ozeki, Mizuki Morita, Hiroshi Yoshimine, Hiroyuki Furusawa, Yoshio Okahata

Analytical Chemistry 79 ( 1 ) 79 - 88 2007年1月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：American Chemical Society

By using a 27-MHz piezoelectric quartz oscillator connected with a vector network analyzer, we obtained resonance frequency decreases (-Delta F-water) and energy dissipation increases (Delta D-water) during binding of biotinylated bovine serum albumin, biotinylated ssDNA, biotinylated dsDNA, and biotinylated pullulan to a NeutrAvidin-immobilized 27-MHz quartz crystal microbalance (QCM) plate in aqueous solution, as well as in the wet air phase (98% humidity, -Delta F-wet and Delta D-wet) and in the dry air phase (-Delta F-air and Delta D-air). -Delta F-water indicates the total mass of the molecule, bound water, and vibrated water in aqueous solutions. -Delta F-wet indicates the total mass of the molecule and bound water. -Delta F-air simply shows the real mass of the molecule on the QCM. In terms of results, (-Delta F-wet)/(-Delta F-air) values indicated the bound water ratios per unit biomolecular mass were on the order of pullulan (2.1-2.2) > DNAs = proteins (1.4-1.6) > polystyrene (1.0). The (-Delta F-water)/(-Delta F-air) values indicated the hydrodynamic water (bound and vibrated water) ratios per unit biomolecular mass were on the order of dsDNA (6.5) > ssDNA = pullulan (3.5-4.4) > proteins (2.4-2.5) > polystyrene (1.0). Energy dissipation parameters per unit mass in water (Delta D-water/(-Delta F-air)) were on the order of pullulan > dsDNA > ssDNA > proteins > polystyrene. Energy dissipation in the wet and dry air phases (Delta D-wet and Delta D-air) were negligibly small, which indicates even these biomolecules act as elastic membranes in the air phase (without aqueous solution). We obtained a good linear relationship between [(-Delta F-water)/(-Delta F-air) - 1], which is indicative of hydration and Delta D-water/(-Delta F-air) of proteins. The aforementioned values suggest that the energy dissipation of proteins was mainly caused by hydration and that proteins themselves are elastic molecules without energy dissipation in aqueous solutions. On the contrary, plots in cases of denatured proteins, DNAs, and pullulans were relatively deviant toward the large hydration and energy dissipation from the theoretical line as perfect elastic materials, meaning that the large energy dissipation occurs because of viscoelastic properties of denatured proteins, linear DNAs, and pullulans in the water phase, in addition to energy dissipation due to the hydration of molecules. These two parameters could characterize various biomolecules with structural properties in aqueous solutions.

DOI： 10.1021/ac060873x

Web of Science

PubMed

researchmap

　前のページ - 次のページ　

<森田 瑞樹>

論文 - 森田 瑞樹

<森田　瑞樹>

論文 - 森田　瑞樹