Search Results - "Takeda, Mayuko"

The Roles of the Sole Activator-Type Auxin Response Factor in Pattern Formation of Marchantia polymorpha by Kato, Hirotaka, Kouno, Masaru, Takeda, Mayuko, Suzuki, Hidemasa, Ishizaki, Kimitsune, Nishihama, Ryuichi, Kohchi, Takayuki

“…Cell division patterning is important to determine body shape in plants. Nuclear auxin signaling mediated by AUXIN RESPONSE FACTOR (ARF) transcription factors…”
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Investigation of HO2 uptake mechanisms onto multiple-component ambient aerosols collected in summer and winter time in Yokohama, Japan by Zhou, Jun, Fukusaki, Yukiko, Murano, Kentaro, Gautam, Tania, Bai, Yu, Inomata, Yoshimi, Komatsu, Hiroaki, Takeda, Mayuko, Yuan, Bin, Shao, Min, Sakamoto, Yosuke, Kajii, Yoshizumi

“…•We developed an offline method to measure HO2 uptake kinetics onto ambient aerosols.•γHO2 is strongly RH and pH dependent and inversely correlated with…”
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Geometrical Conversion of the EGFR Extracellular Domain by Adiabatic Mapping Combining Normal Mode Analysis of the Elastic Network Model and Energy Optimization by Nojima, Hiroyuki, Kiyota, Yasuomi, Terashi, Genki, Takeda-Shitaka, Mayuko, Matsubara, Hajime

“…The activation of epidermal growth factor receptor (EGFR) involves the geometrical conversion of the extracellular domain (ECD) from the tethered to the…”
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Impact of AlphaFold on structure prediction of protein complexes: The CASP15‐CAPRI experiment by Brysbaert, Guillaume, Raouraoua, Nessim, Bates, Paul A., Giulini, Marco, Honorato, Rodrigo V., Noort, Charlotte, Teixeira, Joao M. C., Bonvin, Alexandre M. J. J., Kong, Ren, Shi, Hang, Lu, Xufeng, Chang, Shan, Guo, Zhiye, Chen, Xiao, Roy, Raj S., Wu, Tianqi, Giri, Nabin, Quadir, Farhan, Chen, Chen, Cheng, Jianlin, Del Carpio, Carlos A., Ichiishi, Eichiro, Rodriguez‐Lumbreras, Luis A., Fernandez‐Recio, Juan, Harmalkar, Ameya, Chu, Lee‐Shin, Canner, Sam, Smanta, Rituparna, Gray, Jeffrey J., Li, Hao, Lin, Peicong, He, Jiahua, Tao, Huanyu, Huang, Sheng‐You, Roel‐Touris, Jorge, Jimenez‐Garcia, Brian, Christoffer, Charles W., Jain, Anika J., Kagaya, Yuki, Kannan, Harini, Nakamura, Tsukasa, Terashi, Genki, Zhang, Yuanyuan, Zhang, Zicong, Fujuta, Hayato, Sekijima, Masakazu, Kihara, Daisuke, Khan, Omeir, Kotelnikov, Sergei, Ghani, Usman, Beglov, Dmitri, Vajda, Sandor, Negi, Surendra S., Ricciardelli, Tiziana, Barradas‐Bautista, Didier, Cao, Zhen, Chawla, Mohit, Cavallo, Luigi, Yin, Rui, Guest, Johnathan D., Lee, Jessica, Pierce, Brian G., Shor, Ben, Cohen, Tomer, Halfon, Matan, Schneidman‐Duhovny, Dina, Zhu, Shaowen, Sun, Yuanfei, Shen, Yang, Maszota‐Zieleniak, Martyna, Bojarski, Krzysztof K., Lubecka, Emilia A., Marcisz, Mateusz, Danielsson, Annemarie, Dziadek, Lukasz, Gieldon, Artur, Liwo, Adam, Samsonov, Sergey A., Slusarz, Rafal, Zieba, Karolina, Sieradzan, Adam K., Czaplewski, Cezary, Kobayashi, Shinpei, Miyakawa, Yuta, Kiyota, Yasuomi, Takeda‐Shitaka, Mayuko, Olechnovic, Kliment, Valancauskas, Lukas, Venclovas, Ceslovas, Yang, Lin, Hou, Chengyu, He, Xiaodong, Guo, Shuai, Jiang, Shenda, Ma, Xiaoliang, Duan, Rui, Xu, Xianjin, Zou, Xiaoqin, Velankar, Sameer, Wodak, Shoshana J.

“…We present the results for CAPRI Round 54, the 5th joint CASP‐CAPRI protein assembly prediction challenge. The Round offered 37 targets, including 14…”
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Quality Assessment Methods for 3D Protein Structure Models Based on a Residue–Residue Distance Matrix Prediction by Terashi, Genki, Nakamura, Yuuki, Shimoyama, Hiromitsu, Takeda-Shitaka, Mayuko

“…In the absence of experimentally determined three dimensional (3D) structures of proteins, the prediction of protein structures using computational methods is…”
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CAB-Align: A Flexible Protein Structure Alignment Method Based on the Residue-Residue Contact Area by Terashi, Genki, Takeda-Shitaka, Mayuko

“…Proteins are flexible, and this flexibility has an essential functional role. Flexibility can be observed in loop regions, rearrangements between secondary…”
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Molecular Recognition Study on the Binding of Calcium to Calbindin D9k Based on 3D Reference Interaction Site Model Theory by Kiyota, Yasuomi, Takeda-Shitaka, Mayuko

“…Ca2+-binding proteins are widely distributed throughout cells and play various important roles. Calbindin D9k is a member of the EF-hand Ca2+-binding protein…”
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Identification and characterisation of the anti‐allergic compound from lotus root by Wakugawa, Tomoharu, Nagamine, Kenichi, Hiramatsu, Miharu, Takeda, Mayuko, Kawata, Chika, Kashiwada, Yoshiki, Shinohara, Keiko, Sawada, Eiji, Yabumoto, Masami, Fujino, Hiromichi, Kitamura, Yoshiaki, Fukui, Hiroyuki, Takeda, Noriaki, Mizuguchi, Hiroyuki

“…ABSTRACT Aim Histamine H1 receptor (H1R) gene is up‐regulated in the nasal mucosa of patients with pollinosis, and its expression level is strongly correlated…”
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Fams-ace: A combined method to select the best model after remodeling all server models by Terashi, Genki, Takeda-Shitaka, Mayuko, Kanou, Kazuhiko, Iwadate, Mitsuo, Takaya, Daisuke, Hosoi, Akio, Ohta, Kazuhiro, Umeyama, Hideaki

“…During Critical Assessment of Protein Structure Prediction (CASP7, Pacific Grove, CA, 2006), fams‐ace was entered in the 3D coordinate prediction category as a…”
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Bioinformatics Based Ligand-Docking and in-Silico Screening by Takaya, Daisuke, Takeda-Shitaka, Mayuko, Terashi, Genki, Kanou, Kazuhiko, Iwadate, Mitsuo, Umeyama, Hideaki

“…We report a novel method, ChooseLD (CHOOse biological information Semi-Empirically on the Ligand Docking), which uses simulated annealing (SA) based on…”
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Dynamic Influence of the Two Membrane-Proximal Immunoglobulin-Like Domains upon the Peptide-Binding Platform Domain in Class I and Class II Major Histocompatibility Complexes: Normal Mode Analysis by Nojima, Hiroyuki, Kanou, Kazuhiko, Kamiya, Kenshu, Atsuda, Koichiro, Umeyama, Hideaki, Takeda-Shitaka, Mayuko

“…Major histocompatibility complexes (MHCs) mainly fall into class I and class II. The two classes have similar structures, with two membrane-proximal…”
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LB3D: a protein three-dimensional substructure search program based on the lower bound of a root mean square deviation value by Terashi, Genki, Shibuya, Tetsuo, Takeda-Shitaka, Mayuko

“…Searching for protein structure-function relationships using three-dimensional (3D) structural coordinates represents a fundamental approach for determining…”
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Interaction between the antigen and antibody is controlled by the constant domains: Normal mode dynamics of the HEL–HyHEL‐10 complex by Adachi, Masaaki, Kurihara, Youji, Nojima, Hiroyuki, Takeda‐Shitaka, Mayuko, Kamiya, Kenshu, Umeyama, Hideaki

“…The antigen binding fragment (Fab) of a monoclonal antibody (HyHEL‐10) consists of variable domains (Fv) and constant domains (CL–CH1). Normal modes have been…”
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Dynamic Interaction among the Platform Domain and Two Membrane-Proximal Immunoglobulin-Like Domains of Class I Major Histocompatibility Complex: Normal Mode Analysis by Nojima, Hiroyuki, Takeda-Shitaka, Mayuko, Kanou, Kazuhiko, Kamiya, Kenshu, Umeyama, Hideaki

“…Class I major histocompatibility complex (MHC) molecules have three domains, a platform domain and two membrane-proximal immunoglobulin-like domains, an α3…”
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HUMAN FAMSD-BASE: High Quality Protein Structure Model Database for the Human Genome Using the FAMSD Homology Modeling Method by Kanou, Kazuhiko, Hirata, Tomoko, Iwadate, Mitsuo, Terashi, Genki, Umeyama, Hideaki, Takeda-Shitaka, Mayuko

“…Almost all proteins express their biological functions through the structural conformation of their specific amino acid sequences. Therefore, acquiring the…”
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Method for Predicting Homology Modeling Accuracy from Amino Acid Sequence Alignment: the Power Function by Iwadate, Mitsuo, Kanou, Kazuhiko, Terashi, Genki, Umeyama, Hideaki, Takeda-Shitaka, Mayuko

“…We have devised a power function (PF) that can predict the accuracy of a three-dimensional (3D) structure model of a protein using only amino acid sequence…”
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Evaluation of Homology Modeling of the Severe Acute Respiratory Syndrome (SARS) Coronavirus Main Protease for Structure Based Drug Design by Takeda-Shitaka, Mayuko, Nojima, Hiroyuki, Takaya, Daisuke, Kanou, Kazuhiko, Iwadate, Mitsuo, Umeyama, Hideaki

“…To accelerate the development of drugs against severe acute respiratory syndrome (SARS), we constructed a homology model of the SARS coronavirus main protease…”
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Evaluation of the third solvent clusters fitting procedure for the prediction of protein-protein interactions based on the results at the CAPRI blind docking study by Komatsu, Katsuichiro, Kurihara, Youji, Iwadate, Mitsuo, Takeda-Shitaka, Mayuko, Umeyama, Hideaki

“…To predict protein–protein interactions, rough or coarse handling for the induced fit problem is proposed. Our method involves the overlap of two hydrophobic…”
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Protein structure prediction in structure based drug design by Takeda-Shitaka, Mayuko, Takaya, Daisuke, Chiba, Chieko, Tanaka, Hirokazu, Umeyama, Hideaki

“…The human genome and other genome sequencing projects have generated huge amounts of protein sequence information. Recently, a structural genomics project that…”
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Topology of AspT, the Aspartate:Alanine Antiporter of Tetragenococcus halophilus, Determined by Site-Directed Fluorescence Labeling by NANATANI, Kei, FUJIKI, Takashi, ABE, Keietsu, KANOU, Kazuhiko, TAKEDA-SHITAKA, Mayuko, UMEYAMA, Hideaki, LIWEN YE, XICHENG WANG, NAKAJIMA, Tasuku, UCHIDA, Takafumi, MALONEY, Peter C

“…Article Usage Stats Services JB Citing Articles Google Scholar PubMed Related Content Social Bookmarking CiteULike Delicious Digg Facebook Google+ Mendeley…”
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