Impact of Hydrogen Bonding on P-Glycoprotein Efflux Transport as Revealed by Evaluation of a De Novo Prediction Model

Yulong Gou, Suyong Re, Kenji Mizuguchi, Chioko Nagao

ACS Medicinal Chemistry Letters　2023/12/21　Research paper (scientific journal)

Attention network for predicting T-cell receptor–peptide binding can associate attention with interpretable protein structural properties

Kyohei Koyama, Kosuke Hashimoto, Chioko Nagao, Kenji Mizuguchi

Frontiers in Bioinformatics　Vol. 3　2023/12/18　Research paper (scientific journal)

DruMAP: A Novel Drug Metabolism and Pharmacokinetics Analysis Platform

Hitoshi Kawashima, Reiko Watanabe, Tsuyoshi Esaki, Masataka Kuroda, Chioko Nagao, Yayoi Natsume-Kitatani, Rikiya Ohashi, Hiroshi Komura, Kenji Mizuguchi

Journal of Medicinal Chemistry　2023/07/14　Research paper (scientific journal)

RDFization of Interview Forms for effective use of pharmaceutical documents

Chioko Nagao, Mayumi Kamada, Masahiko Nakatsui, Akiko Fukagawa, Toshiaki Katayama, Shuichi Kawashima, Kenji Mizuguchi, Rika Abe

Japanese Journal of Drug Informatics　Vol. 24　No. 4　p. 187-195　2023/02　Research paper (scientific journal)

Data-driven patient stratification and drug target discovery by using medical information and serum proteome data of idiopathic pulmonary fibrosis patients

Yayoi Natsume-Kitatani, Mari N Itoh, Yoshito Takeda, Masataka Kuroda, Haruhiko Hirata, Kohtaro Miyake, Takayuki Shiroyama, Yuya Shirai, Yoshimi Noda, Yuichi Adachi, Takatoshi Enomoto, Saori Amiya, Jun Adachi, Ryohei Narumi, Satoshi Muraoka, Takeshi Tomonaga, Sadao Kurohashi, Fei Cheng, Ribeka Tanaka, Shuntaro Yada, Eiji Aramaki, Shoko Wakamiya, Yi-An Chen, Chihiro Higuchi, Yosui Nojima, Takeshi Fujiwara, Chioko Nagao, Yasushi Matsumura, Kenji Mizuguchi, Atsushi Kumanogoh, Naonori Ueda

2022/03/29

Developing a Kinase-Specific Target Selection Method Using a Structure-Based Machine Learning Approach.

Arina Afanasyeva, Chioko Nagao, Kenji Mizuguchi

Advances and applications in bioinformatics and chemistry : AABC　Vol. 13　p. 27-40　2020/12　Research paper (scientific journal)

Novel anti-flavivirus drugs targeting the nucleolar distribution of core protein.

Makoto Tokunaga, Yoichi Miyamoto, Tatsuya Suzuki, Mayumi Otani, Shinsuke Inuki, Tsuyoshi Esaki, Chioko Nagao, Kenji Mizuguchi, Hiroaki Ohno, Yoshihiro Yoneda, Toru Okamoto, Masahiro Oka, Yoshiharu Matsuura

Virology　Vol. 541　p. 41-51　2020/02　Research paper (scientific journal)

A prospective compound screening contest identified broader inhibitors for Sirtuin 1.

Shuntaro Chiba, Masahito Ohue, Anastasiia Gryniukova, Petro Borysko, Sergey Zozulya, Nobuaki Yasuo, Ryunosuke Yoshino, Kazuyoshi Ikeda, Woong-Hee Shin, Daisuke Kihara, Mitsuo Iwadate, Hideaki Umeyama, Takaaki Ichikawa, Reiji Teramoto, Kun-Yi Hsin, Vipul Gupta, Hiroaki Kitano, Mika Sakamoto, Akiko Higuchi, Nobuaki Miura, Kei Yura, Masahiro Mochizuki, Chandrasekaran Ramakrishnan, A Mary Thangakani, D Velmurugan, M Michael Gromiha, Itsuo Nakane, Nanako Uchida, Hayase Hakariya, Modong Tan, Hironori K Nakamura, Shogo D Suzuki, Tomoki Ito, Masahiro Kawatani, Kentaroh Kudoh, Sakurako Takashina, Kazuki Z Yamamoto, Yoshitaka Moriwaki, Keita Oda, Daisuke Kobayashi, Tatsuya Okuno, Shintaro Minami, George Chikenji, Philip Prathipati, Chioko Nagao, Attayeb Mohsen, Mari Ito, Kenji Mizuguchi, Teruki Honma, Takashi Ishida, Takatsugu Hirokawa, Yutaka Akiyama, Masakazu Sekijima

Scientific reports　Vol. 9　No. 1　p. 19585-19585　2019/12/20　Research paper (scientific journal)

Development of an in silico prediction system of human renal excretion and clearance from chemical structure information incorporating fraction unbound in plasma as a descriptor.

Reiko Watanabe, Rikiya Ohashi, Tsuyoshi Esaki, Hitoshi Kawashima, Yayoi Natsume-Kitatani, Chioko Nagao, Kenji Mizuguchi

Scientific reports　Vol. 9　No. 1　p. 18782-18782　2019/12/11　Research paper (scientific journal)

Constructing an In Silico Three-Class Predictor of Human Intestinal Absorption With Caco-2 Permeability and Dried-DMSO Solubility.

Tsuyoshi Esaki, Rikiya Ohashi, Reiko Watanabe, Yayoi Natsume-Kitatani, Hitoshi Kawashima, Chioko Nagao, Hiroshi Komura, Kenji Mizuguchi

Journal of pharmaceutical sciences　Vol. 108　No. 11　p. 3630-3639　2019/11　Research paper (scientific journal)

Computational Model To Predict the Fraction of Unbound Drug in the Brain.

Tsuyoshi Esaki, Rikiya Ohashi, Reiko Watanabe, Yayoi Natsume-Kitatani, Hitoshi Kawashima, Chioko Nagao, Kenji Mizuguchi

Journal of chemical information and modeling　Vol. 59　No. 7　p. 3251-3261　2019/07/22　Research paper (scientific journal)

High-Contrast Facile Imaging with Target-Directing Fluorescent Molecular Rotors, the N3-Modified Thioflavin T Derivatives.

Yuka Kataoka, Hiroto Fujita, Arina Afanaseva, Chioko Nagao, Kenji Mizuguchi, Yuuya Kasahara, Satoshi Obika, Masayasu Kuwahara

Biochemistry　Vol. 58　No. 6　p. 493-498　2019/02/12　Research paper (scientific journal)

Prediction of the secondary structure of short DNA aptamers.

Arina Afanasyeva, Chioko Nagao, Kenji Mizuguchi

Biophysics and physicobiology　Vol. 16　p. 287-294　2019　Research paper (scientific journal)

Predicting Fraction Unbound in Human Plasma from Chemical Structure: Improved Accuracy in the Low Value Ranges.

Watanabe R, Esaki T, Kawashima H, Natsume-Kitatani Y, Nagao C, Ohashi R, Mizuguchi K

Molecular pharmaceutics　Vol. 15　No. 11　p. 5302-5311　2018/11　Research paper (scientific journal)

Data Curation can Improve the Prediction Accuracy of Metabolic Intrinsic Clearance.

Esaki T, Watanabe R, Kawashima H, Ohashi R, Natsume-Kitatani Y, Nagao C, Mizuguchi K

Molecular informatics　Vol. 38　No. 1-2　2018/09　Research paper (scientific journal)

Development of a pharmacokinetics prediction system using multiscale integrated modeling: 2. Classification of aqueous solubility measured using the dried-DMSO method

Tsuyoshi Esaki, Reiko Watanabe, Hitoshi Kawashima, Yayoi Natsume-Kitatani, Chioko Nagao, Rikiya Ohashi, Kenji Mizuguchi

Chem-Bio Informatics Society Annual Meeting　2017/10

Improved pose and affinity predictions using different protocols tailored on the basis of data availability

Philip Prathipati, Chioko Nagao, Shandar Ahmad, Kenji Mizuguchi

JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN　Vol. 30　No. 9　p. 817-828　2016/09　Research paper (scientific journal)

Dextran sulfate-resistant A/Puerto Rico/8/34 influenza virus is associated with the emergence of specific mutations in the neuraminidase glycoprotein

Hiroshi Yamada, Chioko Nagao, Ahmad M. Haredy, Yasuko Mori, Kenji Mizuguchi, Koichi Yamanishi, Shigefumi Okamoto

ANTIVIRAL RESEARCH　Vol. 111　p. 69-77　2014/11　Research paper (scientific journal)

Crystal structure of FtsA from Staphylococcus aureus

Junso Fujita, Yoko Maeda, Chioko Nagao, Yuko Tsuchiya, Yuma Miyazaki, Mika Hirose, Eiichi Mizohata, Yoshimi Matsumoto, Tsuyoshi Inoue, Kenji Mizuguchi, Hiroyoshi Matsumura

FEBS LETTERS　Vol. 588　No. 10　p. 1879-1885　2014/05　Research paper (scientific journal)

Prediction of Detailed Enzyme Functions and Identification of Specificity Determining Residues by Random Forests

Chioko Nagao, Nozomi Nagano, Kenji Mizuguchi

PLOS ONE　Vol. 9　No. 1　2014/01　Research paper (scientific journal)

Expression, purification, crystallization and preliminary crystallographic study of FtsA from methicillin-resistant Staphylococcus aureus

Junso Fujita, Yuma Miyazaki, Mika Hirose, Chioko Nagao, Eiichi Mizohata, Yoshimi Matsumoto, Kenji Mizuguchi, Tsuyoshi Inoue, Hiroyoshi Matsumura

ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY AND CRYSTALLIZATION COMMUNICATIONS　Vol. 69　No. Pt 8　p. 895-898　2013/08　Research paper (scientific journal)

Computational design, construction, and characterization of a set of specificity determining residues in protein-protein interactions

Chioko Nagao, Nozomi Izako, Shinji Soga, Samia Haseeb Khan, Shigeki Kawabata, Hiroki Shirai, Kenji Mizuguchi

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS　Vol. 80　No. 10　p. 2426-2436　2012/10　Research paper (scientific journal)

Sagace: A web-based search engine for biomedical databases in Japan

Mizuki Morita, Yoshinobu Igarashi, Maori Ito, Yi-An Chen, Chioko Nagao, Yuki Sakaguchi, Ryuichi Sakate, Tohru Masui, Kenji Mizuguchi

BMC Research Notes　Vol. 5　2012　Research paper (scientific journal)

Detecting subtle functional differences in ketopantoate reductase and related enzymes using a rule-based approach with sequence-structure homology recognition scores

Sukanta Mondal, Chioko Nagao, Kenji Mizuguchi

PROTEIN ENGINEERING DESIGN & SELECTION　Vol. 23　No. 11　p. 859-869　2010/11　Research paper (scientific journal)

Relationships between functional subclasses and information contained in active-site and ligand-binding residues in diverse superfamilies

Chioko Nagao, Nozomi Nagano, Kenji Mizuguchi

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS　Vol. 78　No. 10　p. 2369-2384　2010/08　Research paper (scientific journal)

Creation of lysine-deficient mutant lymphotoxin-alpha with receptor selectivity by using a phage display system

Yasuo Yoshioka, Hikaru Watanabe, Tomohiro Morishige, Xinglei Yao, Shinji Ikemizu, Chioko Nagao, Shandar Ahmad, Kenji Mizuguchi, Shin-ichi Tsunoda, Yasuo Tsutsumi, Yohei Mukai, Naoki Okada, Shinsaku Nakagawa

BIOMATERIALS　Vol. 31　No. 7　p. 1935-1943　2010/03　Research paper (scientific journal)

Bioinformatics Approaches for Analysis of Protein-Ligand Interactions

Munazah Andrabi, Chioko Nagao, Kenji Mizuguchi, Shandar Ahmad

Pharmaceutical Data Mining: Approaches and Applications for Drug Discovery　p. 267-299　2009/12/01

Creation of lysine-deficient mutant lymphotoxin-alpha with receptor selectivity by using phage display

Yasuo Yoshioka, Hikaru Watanabe, Tomohiro Morishige, Xinglei Yao, Shinji Ikemizu, Chioko Nagao, Shandar Ahmad, Kenji Mizuguchi, Yasuo Tsutsumi, Yohei Mukai, Naoki Okada, Shinsaku Nakagawa

CYTOKINE　Vol. 48　No. 1-2　p. 111-111　2009/10

Correlation between evolutionary structural development and protein folding

C Nagao, TP Terada, T Yomo, M Sasai

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA　Vol. 102　No. 52　p. 18950-18955　2005/12　Research paper (scientific journal)

Observation of the highly excited vibrational levels of HCP: Application of IR-UV-SEP triple resonance spectroscopy

H Ishikawa, C Nagao, N Mikami

CHEMISTRY LETTERS　No. 9　p. 941-942　1999/09　Research paper (scientific journal)

Observation of the nu(CH) excited vibrational levels in the (A)over-tilde(1)A '' state of HCP by IR-UV double resonance spectroscopy

H Ishikawa, C Nagao, N Mikami

JOURNAL OF MOLECULAR SPECTROSCOPY　Vol. 194　No. 1　p. 52-60　1999/03　Research paper (scientific journal)

Spectroscopic investigation af the generation of "isomerization" states: Eigenvector analysis of the bend-CP stretch polyad

H Ishikawa, C Nagao, N Mikami, RW Field

JOURNAL OF CHEMICAL PHYSICS　Vol. 109　No. 2　p. 492-503　1998/07　Research paper (scientific journal)

Observation of the ''isomerization states'' of HCP by stimulated emission pumping spectroscopy: Comparison between theory and experiment

H Ishikawa, C Nagao, N Mikami, RW Field

JOURNAL OF CHEMICAL PHYSICS　Vol. 106　No. 7　p. 2980-2983　1997/02　Research paper (scientific journal)