CiNii Articles

1

INVESTIGATION OF ACCURACY OF OCEAN RADAR CURRNETS UPDATED SINCE 2016 IN THE ISE BAY [in Japanese]

TSUBONO Takaki , MISUMI Kazuhiro , TSUMUNE Daisuke

… The comparison showed that the RMSD (:Root Mean Square Deviation) between the simulation and recent averages was less than that of the previous averages, suggesting that the updates since 2016 could probably provide the velocities with higher quality in the Ise Bay. …

Journal of Japan Society of Civil Engineers, Ser. B2 (Coastal Engineering) 76(2), I_1369-I_1374, 2020

J-STAGE
2

Elucidation of the Role of Ca2+ in the Formation of an RNA Aptamer/Human Immunoglobulin G Complex Using Molecular Dynamics Simulation [in Japanese]

ISHII Seiichiro , SEKIGUCHI Masahiro , YOSHIDA Hisae , MASUKAWA Keisuke , ISHIKAWA Takeshi , SAKAMOTO Taiichi , YAMAGISHI Kenji

… ions, the RMSD of the RNA aptamer backbone remained below approximately 3.0 Å from the crystal structure during a 1,500-ns simulation. … ions, the RMSD increased and the structure of the RNA aptamer changed from the initial structure. …

Journal of Computer Chemistry, Japan 18(5), 208-210, 2019

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3

Construction of Band Gap Prediction Model for π-conjugated Polymers Using Aromatic/Quinoid and Donor/Acceptor Properties [in Japanese]

HAYASHI Yoshihiro , KAWAUCHI Susumu

… The neural network, which was constructed by 2 hidden layers with 5 neurons per layer, quantitatively predicts (RMSD = 0.207 eV, R2 …

Journal of Computer Chemistry, Japan 18(5), 224-226, 2019

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4

More efficient screening of protein-protein complex model structures for reducing the number of candidates

Takemura Kazuhiro , Kitao Akio

… We introduced the three metrics ligand-root-mean-square deviation (L-RMSD), interface-ligand-RMSD (iL-RMSD), and the fraction of common contacts (FCC), and examined various ranges of cut-offs for clusters to determine the best set of clustering parameters. … Using iL-RMSD with a cut-off radius of 8 Å, the number of decoys that contain at least one near-native model with 90% probability decreased from 4,808 to 320, a 93% reduction in the original number of decoys. …

Biophysics and Physicobiology 16(0), 295-303, 2019

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5

Statistical Evaluation of Monthly Marine Surface Winds of CMIP6 GCMs in the western North Pacific

BADRIANA M. R. , LEE H.S.

… The surface winds are evaluated by using five statistics, bias, correlation coefficient (R), root mean square deviation (RMSD), standard deviation (σ) and Index of Agreement (IoA). … RMSD and standard deviation on average is relatively similar for each GCM and ensemble. …

Journal of Japan Society of Civil Engineers, Ser. B2 (Coastal Engineering) 75(2), I_1219-I_1224, 2019

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6

Efficient Approximate 3-Dimensional Point Set Matching Using Root-Mean-Square Deviation Score

SASAKI Yoichi , SHIBUYA Tetsuo , ITO Kimihito , ARIMURA Hiroki

… In this paper, we study the approximate point set matching (APSM) problem with minimum RMSD score under translation, rotation, and one-to-one correspondence in d-dimension. … First, we present an efficient branch-and-bound algorithm using a novel lower bound function of the minimum RMSD score for the enumeration version of APSM problem. …

IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences E102.A(9), 1159-1170, 2019

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7

Statistical Analysis of Optimized Isotherm Model for Maxsorb III/Ethanol and Silica Gel/Water Pairs

Rahman Md. Matiar , Pal Animesh , Uddin Kutub , Thu Kyaw , Saha Bidyut Baran

… However, RMSD for Redlich-Peterson and SSE for Tòth are appropriate for Maxsorb III/ethanol and silica gel/water pairs, respectively. …

Evergreen 5(4), 1-12, 2018-12

IR DOI
8

正規化ハミング距離を用いた三次元点集合マッチングの高速化とインフルエンザウイルス解析への応用 [in Japanese]

佐々木耀一 , 渋谷哲朗 , 大森亮介 , 伊藤公人 , 有村博紀

… 我々は三次元点集合のマッチング問題に対する高速なアルゴリズムを提案した．点集合の構造の類似距離にはRMSDを用い，構造以外の情報である文字(ラベル)情報を利用して，本問題を高速化することを考えた．実験ではインフルエンザウイルスに対して，構造距離と文字列距離の相関関係を調べ，枝刈り関数を提案し，アルゴリズムの精度の保証も確かめた． …

第79回全国大会講演論文集 2017(1), 617-618, 2017-03-16

IPSJ
9

Structural and functional insights into thermally stable cytochrome c' from a thermophile

Fujii Sotaro , Oki Hiroya , Kawahara Kazuki , Yamane Daisuke , Yamanaka Masaru , Maruno Takahiro , Kobayashi Yuji , Masanari Misa , Wakai Satoshi , Nishihara Hirofumi , Ohkubo Tadayasu , Sambongi Yoshihiro

This work was performed under the Cooperative Research Program of the "Network Joint Research Center for Materials and Devices".

Protein Science 26(4), 737-748, 2017-03-06

IR
10

Prediction of the site of CYP3A4 metabolism of tolterodine by molecular dynamics simulation from multiple initial structures of the CYP3A4-tolterodine complex

Sato Atsuko , Yuki Hitomi , Watanabe Chiduru , Saito Jun-ichi , Konagaya Akihiko , Honma Teruki

CYP3A4 contributes to the metabolism of more than 30% of drugs in clinical use. Predicting the sites of metabolism (SOM) by CYP3A4, as well as the binding modes, for target compounds is impor …

Chem-Bio Informatics Journal 17(0), 38-52, 2017

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11

Dynamic Specification of Initial Structures in Parallel Cascade Selection Molecular Dynamics (PaCS-MD) Efficiently Promotes Biologically Relevant Rare Events

Harada Ryuhei , Shigeta Yasuteru

… PaCS-MD typically has a fixed ninitial, while in dn-PaCS-MD it is dynamically reset according to a minimum root mean square deviation (RMSD), defined as an RMSD derivative. …

Bulletin of the Chemical Society of Japan 90(11), 1236-1243, 2017

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12

Molecular Dynamic Studies of Interferon and Innate Immunity Resistance in MERS CoV Non-Structural Protein 3

Alfuwaires Manal , Altaher Abdallah , Kandeel Mahmoud

… There were marked changes in the root-mean-square deviation (RMSD) in the ubiquitin like domain (Ubl) and the fingers subdomain of the catalytic domain of Plpro. …

Biological and Pharmaceutical Bulletin 40(3), 345-351, 2017

J-STAGE Ichushi Web
13

A Fast Convergent Simulated Annealing Algorithm for Protein-Folding: Simulated Annealing Outlier FLOODing (SA-OFLOOD) Method

Harada Ryuhei , Nakamura Tomotake , Shigeta Yasuteru

… root mean square deviation (RMSD) with only 200 ns simulation time. … RMSD), indicating the strength of SA-OFLOOD on the protein-folding problem. … RMSD of 1.0 Å through a nanosecond-order simulation time. …

Bulletin of the Chemical Society of Japan 89(11), 1361-1367, 2016

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14

Study of molecular recognition mechanism in protein GPI modification: a bioinformatics analysis of interaction between GPI-anchored proteins and modification enzyme

MUKAI Yuri , TAKAHASHI Daiki , OGAWA Tsubasa , HAMADA Kota , ETCHUYA Kenji

… In particular, the direct interaction between ω-sites of GPI-anchored proteins and PIG-K was focused on, the root-mean-square deviation (RMSD) and three-dimensional amino acid propensity around the ω-sites were analyzed in the present study. …

Journal of Biomechanical Science and Engineering 11(1), 15-00361-15-00361, 2016

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15

Using Bregmann Divergence Regularized Machine for Comparison of Molecular Local Structures

RELATOR Raissa , NAGANO Nozomi , KATO Tsuyoshi

… For the comparison, the root mean square deviation (RMSD) has been used as a conventional index. …

IEICE Transactions on Information and Systems E99.D(1), 275-278, 2016

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16

Efficient Approximate 3-Dimensional Point Set Matching and Its Application to Molecular Pattern Matching [in Japanese]

佐々木耀一 , 渋谷哲朗 , 伊藤公人 [他]

電子情報通信学会技術研究報告 = IEICE technical report : 信学技報 115(112), 335-341, 2015-06-23
17

Efficient Approximate 3-Dimensional Point Set Matching and Its Application to Molecular Pattern Matching [in Japanese]

佐々木耀一 , 渋谷哲朗 , 伊藤公人 [他]

電子情報通信学会技術研究報告 = IEICE technical report : 信学技報 115(111), 219-225, 2015-06-23
18

Molecular Dynamics Simulation with Principle Component Analysis Study on the Dynamics of DHFR Protein from Moritella profunda at High Pressure Condition [in Japanese]

米澤康滋

… We took a trajectory from the simulations and performed several analyses involving RMSD, RMSF, Gyration and principle component analysis（PCA）. …

Memoirs of Institute of Advanced Technology, Kinki University (20), 9-18, 2015-03

IR
19

Validation of AMSR2 Sea Surface Wind and Temperature over the Kuroshio Extension Region

Tomita Hiroyuki , Kawai Yoshimi , Cronin Meghan F. , Hihara Tsutomu , Kubota Masahisa

… From the year-long comparison, we confirm that the root mean square difference (RMSD) of AMSR2 SST observations was 0.75°C and meets the criterion for release accuracy (0.8°C). … On the other hand, the RMSD of SSW was 1.6 m s−1, slightly worse than the criterion (1.5 m s−1), suggesting that the algorithm for SSW needs to be further improved. …

SOLA 11(0), 43-47, 2015

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20

Computational Simulation Study on Proteins Under High Pressure Condition : A Molecular Dynamics Study on DHFR enzyme [in Japanese]

米澤康滋

… The resultsincluding RMSD, Radius of Gyration, Distance map, clearly show that pressure does not much impact on the global averaged static properties of DHFR. …

Memoirs of Institute of Advanced Technology, Kinki University (19), 25-33, 2014-03

IR

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