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Takeshi Kawabata

Section

Graduate School of Information Sciences

Job title

Specially Appointed Associate Professor(Research)

Degree

博士（農学）（東京大学）
修士（農学）（東京大学）

researchmap

https://researchmap.jp/kawabata1997

J-GLOBAL ID

201901004207398307

e-Rad No.

60343274

Profile

1992年(平成4年)3月: 東京大学工学部精密機械工学科卒業
1997年(平成9年)3月: 東京大学農学生命科学研究科応用生命工学専攻博士課程修了。博士（農学）取得指導教員：清水謙多郎教授
1997年(平成9年)4月: 国立遺伝学研究所COE研究員（指導教員：西川建教授)
1999年(平成11年)4月: 科学技術振興事業団( 国立遺伝学研究所で研究に従事) 博士研究員（指導教員：西川建教授)
2000年(平成12年)7月 :日本学術振興会特別研究員( 国立遺伝学研究所で研究に従事) 博士研究員（指導教員：西川建教授)
2001年 (平成13年)10月: 奈良先端科学技術大学院大学情報科学研究科研究員（科学技術振興）（客員助教授）
2006年(平成18年)4月:奈良先端科学技術大学院大学情報科学研究科助教授（任期５年）
2011年(平成23年)4月: 大阪大学蛋白質研究所特任研究員（客員准教授）
2016年(平成28年)6月: 大阪大学蛋白質研究所寄附研究部門准教授（招へい准教授）
2018年(平成30年)4月: 大阪大学蛋白質研究所特任准教授（招へい准教授）

2021年(令和 3年)4月: 蛋白質研究奨励会研究員, 大阪大学大学院生命機能研究科招へい准教授
2022年(令和 4年)4月: 東北大学大学院　情報科学研究科　特任准教授 (木下・大林・西研究室)

Professional Memberships 3

JAPANESE SOCIETY FOR BIOINFORMATICS
PROTEIN SCIENCE SOCIETY OF JAPAN
THE BIOPHYSICAL SOCIETY OF JAPAN

Research Areas 1

Life sciences / Biophysics /

Awards 1

Award for Outstanding Biophysics and Physicobiology Paper

2017/09　The Biophysical Society of Japan　Takeshi Kawabata, Yusuke Sugihara, Yoshifumi Fukunishi, Haruki Nakamura "LigandBox: A database for 3D structures of chemical compounds" BIOPHYSICS Vol.9 pp.113-121 (2013)

Papers 72

Assessing Structural Classification Using AlphaFold2 Models Through ECOD‐Based Comparative Analysis Peer-reviewed

Takeshi Kawabata, Kengo Kinoshita

Proteins: Structure, Function, and Bioinformatics　2025/04/19
Publisher: Wiley
DOI： 10.1002/prot.26828 　

ISSN： 0887-3585

eISSN： 1097-0134

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ABSTRACT Identifying homologous proteins is a fundamental task in structural bioinformatics. While AlphaFold2 has revolutionized protein structure prediction, the extent to which structure comparison of its models can reliably detect homologs remains unclear. In this study, we evaluate the feasibility of homology detection using AlphaFold2‐predicted structures through structural comparisons. We considered the classification of the ECOD database for experimental structures as the correct standard and obtained their corresponding predicted models from AlphaFoldDB. To ensure blind assessment, we divided the structures into test and train sets according to their release date. Predicted and experimental 3D structures in the test and train sets were compared using 3D structure comparisons (MATRAS, Dali, and Foldseek) and sequence comparisons (BLAST and HHsearch). The results were evaluated based on the homology annotations in the ECOD database. For top‐1 accuracy, the performance of structural comparisons was comparable to that of HHsearch. However, when considering metrics that included all structural pairs, including more remote homology, structural comparisons outperformed HHsearch. No significant differences were observed between comparisons of experimental versus experimental, predicted versus experimental, and predicted versus predicted structures with pLDDT (prediction confidence) values greater than 60. We also demonstrate that predicted protein structures, determined by NMR, had lower pLDDT values and contained fewer coils than their experimental counterparts. These findings highlight the potential of AlphaFold2 models in structural classification and suggest that 3D structural searches should be conducted not only against the PDB but also against AlphaFoldDB to identify more potential homologs.
Effect of Organic Anion Transporting Polypeptide 1B1 on Plasma Concentration Dynamics of Clozapine in Patients with Treatment-Resistant Schizophrenia Peer-reviewed

Toshihiro Sato, Takeshi Kawabata, Masaki Kumondai, Nagomi Hayashi, Hiroshi Komatsu, Yuki Kikuchi, Go Onoguchi, Yu Sato, Kei Nanatani, Masahiro Hiratsuka, Masamitsu Maekawa, Hiroaki Yamaguchi, Takaaki Abe, Hiroaki Tomita, Nariyasu Mano

International Journal of Molecular Sciences　25　(23)　13228-13228　2024/12/09
Publisher: MDPI AG
DOI： 10.3390/ijms252313228 　

eISSN： 1422-0067

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The involvement of drug-metabolizing enzymes and transporters in plasma clozapine (CLZ) dynamics has not been well examined in Japanese patients with treatment-resistant schizophrenia (TRS). Therefore, this clinical study investigated the relationship between single nucleotide polymorphisms (SNPs) of various pharmacokinetic factors (drug-metabolizing enzymes and transporters) and dynamic changes in CLZ. Additionally, we aimed to determine whether CLZ acts as a substrate for pharmacokinetic factors using in vitro assays and molecular docking calculations. We found that 6 out of 10 patients with TRS and with multiple organic anion transporting polypeptide (OATP) variants (OATP1B1: *1b, *15; OATP1B3: 334T>G, 699G>A; and OATP2B1: *3, 935G>A, 601G>A, 76_84del) seemed to be highly exposed to CLZ and/or N-desmethyl CLZ. A CLZ uptake study using OATP-expressing HEK293 cells showed that CLZ was a substrate of OATP1B1 with Km and Vmax values of 38.9 µM and 2752 pmol/mg protein/10 min, respectively. The results of molecular docking calculations supported the differences in CLZ uptake among OATP molecules and the weak inhibitory effect of cyclosporine A, which is a strong inhibitor of OATPs, on CLZ uptake via OATP1B1. This is the first study to show that CLZ is an OATP1B1 substrate and that the presence of SNPs in OATPs potentially alters CLZ pharmacokinetic parameters.
Engineered polyethylene terephthalate hydrolases: perspectives and limits Peer-reviewed

Fusako Kawai, Ryo Iizuka, Takeshi Kawabata

Applied Microbiology and Biotechnology　108　(1)　2024/07/02
Publisher: Springer Science and Business Media LLC
DOI： 10.1007/s00253-024-13222-2 　

ISSN： 0175-7598

eISSN： 1432-0614

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Abstract Polyethylene terephthalate (PET) is a major component of plastic waste. Enzymatic PET hydrolysis is the most ecofriendly recycling technology. The biorecycling of PET waste requires the complete depolymerization of PET to terephthalate and ethylene glycol. The history of enzymatic PET depolymerization has revealed two critical issues for the industrial depolymerization of PET: industrially available PET hydrolases and pretreatment of PET waste to make it susceptible to full enzymatic hydrolysis. As none of the wild-type enzymes can satisfy the requirements for industrialization, various mutational improvements have been performed, through classical technology to state-of-the-art computational/machine-learning technology. Recent engineering studies on PET hydrolases have brought a new insight that flexibility of the substrate-binding groove may improve the efficiency of PET hydrolysis while maintaining sufficient thermostability, although the previous studies focused only on enzymatic thermostability above the glass transition temperature of PET. Industrial biorecycling of PET waste is scheduled to be implemented, using micronized amorphous PET. Next stage must be the development of PET hydrolases that can efficiently degrade crystalline parts of PET and expansion of target PET materials, not only bottles but also textiles, packages, and microplastics. This review discusses the current status of PET hydrolases, their potential applications, and their profespectal goals. Key points • PET hydrolases must be thermophilic, but their operation must be below 70 °C • Classical and state-of-the-art engineering approaches are useful for PET hydrolases • Enzyme activity on crystalline PET is most expected for future PET biorecycling Graphical Abstract
Structural Perspective of NR4A Nuclear Receptor Family and Their Potential Endogenous Ligands Peer-reviewed

Ryoichi Hashida, Takeshi Kawabata

Biological and Pharmaceutical Bulletin　47　(3)　580-590　2024/03/01
Publisher: Pharmaceutical Society of Japan
DOI： 10.1248/bpb.b23-00600 　

ISSN： 0918-6158

eISSN： 1347-5215
Identification of ultra-rare disruptive variants in voltage-gated calcium channel-encoding genes in Japanese samples of schizophrenia and autism spectrum disorder. International-journal Peer-reviewed

Chenyao Wang, Shin-Ichiro Horigane, Minoru Wakamori, Shuhei Ueda, Takeshi Kawabata, Hajime Fujii, Itaru Kushima, Hiroki Kimura, Kanako Ishizuka, Yukako Nakamura, Yoshimi Iwayama, Masashi Ikeda, Nakao Iwata, Takashi Okada, Branko Aleksic, Daisuke Mori, Takashi Yoshida, Haruhiko Bito, Takeo Yoshikawa, Sayaka Takemoto-Kimura, Norio Ozaki

Translational psychiatry　12　(1)　84-84　2022/02/26

DOI： 10.1038/s41398-022-01851-y 　

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Several large-scale whole-exome sequencing studies in patients with schizophrenia (SCZ) and autism spectrum disorder (ASD) have identified rare variants with modest or strong effect size as genetic risk factors. Dysregulation of cellular calcium homeostasis might be involved in SCZ/ASD pathogenesis, and genes encoding L-type voltage-gated calcium channel (VGCC) subunits Cav1.1 (CACNA1S), Cav1.2 (CACNA1C), Cav1.3 (CACNA1D), and T-type VGCC subunit Cav3.3 (CACNA1I) recently were identified as risk loci for psychiatric disorders. We performed a screening study, using the Ion Torrent Personal Genome Machine (PGM), of exon regions of these four candidate genes (CACNA1C, CACNA1D, CACNA1S, CACNA1I) in 370 Japanese patients with SCZ and 192 with ASD. Variant filtering was applied to identify biologically relevant mutations that were not registered in the dbSNP database or that have a minor allele frequency of less than 1% in East-Asian samples from databases; and are potentially disruptive, including nonsense, frameshift, canonical splicing site single nucleotide variants (SNVs), and non-synonymous SNVs predicted as damaging by five different in silico analyses. Each of these filtered mutations were confirmed by Sanger sequencing. If parental samples were available, segregation analysis was employed for measuring the inheritance pattern. Using our filter, we discovered one nonsense SNV (p.C1451* in CACNA1D), one de novo SNV (p.A36V in CACNA1C), one rare short deletion (p.E1675del in CACNA1D), and 14 NSstrict SNVs (non-synonymous SNV predicted as damaging by all of five in silico analyses). Neither p.A36V in CACNA1C nor p.C1451* in CACNA1D were found in 1871 SCZ cases, 380 ASD cases, or 1916 healthy controls in the independent sample set, suggesting that these SNVs might be ultra-rare SNVs in the Japanese population. The neuronal splicing isoform of Cav1.2 with the p.A36V mutation, discovered in the present study, showed reduced Ca2+-dependent inhibition, resulting in excessive Ca2+ entry through the mutant channel. These results suggested that this de novo SNV in CACNA1C might predispose to SCZ by affecting Ca2+ homeostasis. Thus, our analysis successfully identified several ultra-rare and potentially disruptive gene variants, lending partial support to the hypothesis that VGCC-encoding genes may contribute to the risk of SCZ/ASD.
Protein Data Bank Japan: Celebrating our 20th anniversary during a global pandemic as the Asian hub of three dimensional macromolecular structural data. International-journal Peer-reviewed

Gert-Jan Bekker, Masashi Yokochi, Hirofumi Suzuki, Yasuyo Ikegawa, Takeshi Iwata, Takahiro Kudou, Kei Yura, Toshimichi Fujiwara, Takeshi Kawabata, Genji Kurisu

Protein science : a publication of the Protein Society　31　(1)　173-186　2022/01

DOI： 10.1002/pro.4211 　

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Protein Data Bank Japan (PDBj), a founding member of the worldwide Protein Data Bank (wwPDB) has accepted, processed and distributed experimentally determined biological macromolecular structures for 20 years. During that time, we have continuously made major improvements to our query search interface of PDBj Mine 2, the BMRBj web interface, and EM Navigator for PDB/BMRB/EMDB entries. PDBj also serves PDB-related secondary database data, original web-based modeling services such as Homology modeling of complex structure (HOMCOS), visualization services and utility tools, which we have continuously enhanced and expanded throughout the years. In addition, we have recently developed several unique archives, BSM-Arc for computational structure models, and XRDa for raw X-ray diffraction images, both of which promote open science in the structural biology community. During the COVID-19 pandemic, PDBj has also started to provide feature pages for COVID-19 related entries across all available archives at PDBj from raw experimental data and PDB structural data to computationally predicted models, while also providing COVID-19 outreach content for high school students and teachers.
Difference of binding modes among three ligands to a receptor mSin3B corresponding to their inhibitory activities Peer-reviewed

Tomonori Hayami, Narutoshi Kamiya, Kota Kasahara, Takeshi Kawabata, Jun-ichi Kurita, Yoshifumi Fukunishi, Yoshifumi Nishimura, Haruki Nakamura, Junichi Higo

Scientific Reports　11　(1)　2021/12
Publisher: Springer Science and Business Media LLC
DOI： 10.1038/s41598-021-85612-9 　

eISSN： 2045-2322

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<title>Abstract</title>A preceding experiment suggested that a compound, which inhibits binding of the REST/NRSF segment to the cleft of a receptor protein mSin3B, can be a potential drug candidate to ameliorate many neuropathies. We have recently developed an enhanced conformational sampling method, genetic-algorithm-guided multi-dimensional virtual-system-coupled canonical molecular dynamics, and in the present study, applied it to three systems consisting of mSin3B and one of three compounds, sertraline, YN3, and acitretin. Other preceding experiments showed that only sertraline inhibits the binding of REST/NRSF to mSin3B. The current simulation study produced the spatial distribution of the compounds around mSin3B, and showed that sertraline and YN3 bound to the cleft of mSin3B with a high propensity, although acitretin did not. Further analyses of the simulation data indicated that only the sertraline–mSin3B complex produced a hydrophobic core similar to that observed in the molecular interface of the REST/NRSF-mSin3B complex: An aromatic ring of sertraline sunk deeply in the mSin3B’s cleft forming a hydrophobic core contacting to hydrophobic amino-acid residues located at the bottom of the cleft. The present study proposes a step to design a compound that inhibits competitively the binding of a ligand to its receptor.
Functional characterization of rare NRXN1 variants identified in autism spectrum disorders and schizophrenia International-journal Peer-reviewed

Kanako Ishizuka, Tomoyuki Yoshida, Takeshi Kawabata, Ayako Imai, Hisashi Mori, Hiroki Kimura, Toshiya Inada, Yuko Okahisa, Jun Egawa, Masahide Usami, Itaru Kushima, Mako Morikawa, Takashi Okada, Masashi Ikeda, Aleksic Branko, Daisuke Mori, Toshiyuki Someya, Nakao Iwata, Norio Ozaki

Journal of Neurodevelopmental Disorders　12　(1)　25-25　2020/12
Publisher: Springer Science and Business Media LLC
DOI： 10.1186/s11689-020-09325-2 　

ISSN： 1866-1947

eISSN： 1866-1955

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<title>Abstract</title> <sec> <title>Background</title> Rare genetic variants contribute to the etiology of both autism spectrum disorder (ASD) and schizophrenia (SCZ). Most genetic studies limit their focus to likely gene-disrupting mutations because they are relatively easier to interpret their effects on the gene product. Interpretation of missense variants is also informative to some pathophysiological mechanisms of these neurodevelopmental disorders; however, their contribution has not been elucidated because of relatively small effects. Therefore, we characterized missense variants detected in <italic>NRXN1</italic>, a well-known neurodevelopmental disease-causing gene, from individuals with ASD and SCZ. </sec> <sec> <title>Methods</title> To discover rare variants with large effect size and to evaluate their role in the shared etiopathophysiology of ASD and SCZ, we sequenced <italic>NRXN1</italic> coding exons with a sample comprising 562 Japanese ASD and SCZ patients, followed by a genetic association analysis in 4273 unrelated individuals. Impact of each missense variant detected here on cell surface expression, interaction with NLGN1, and synaptogenic activity was analyzed using an in vitro functional assay and in silico three-dimensional (3D) structural modeling. </sec> <sec> <title>Results</title> Through mutation screening, we regarded three ultra-rare missense variants (T737M, D772G, and R856W), all of which affected the LNS4 domain of <italic>NRXN1</italic>α isoform<italic>,</italic> as disease-associated variants. Diagnosis of individuals with T737M, D772G, and R856W was 1ASD and 1SCZ, 1ASD, and 1SCZ, respectively. We observed the following phenotypic and functional burden caused by each variant. (i) D772G and R856W carriers had more serious social disabilities than T737M carriers. (ii) In vitro assay showed reduced cell surface expression of NRXN1α by D772G and R856W mutations. In vitro functional analysis showed decreased NRXN1α-NLGN1 interaction of T737M and D772G mutants. (iii) In silico 3D structural modeling indicated that T737M and D772G mutations could destabilize the rod-shaped structure of LNS2-LNS5 domains, and D772G and R856W could disturb N-glycan conformations for the transport signal. </sec> <sec> <title>Conclusions</title> The combined data suggest that missense variants in <italic>NRXN1</italic> could be associated with phenotypes of neurodevelopmental disorders beyond the diagnosis of ASD and/or SCZ. </sec>
Molecular Interaction Mechanism of a 14-3-3 Protein with a Phosphorylated Peptide Elucidated by Enhanced Conformational Sampling International-journal Peer-reviewed

Junichi Higo, Takeshi Kawabata, Ayumi Kusaka, Kota Kasahara, Narutoshi Kamiya, Ikuo Fukuda, Kentaro Mori, Yutaka Hata, Yoshifumi Fukunishi, Haruki Nakamura

Journal of Chemical Information and Modeling　60　(10)　4867-4880　2020/10/26
Publisher: American Chemical Society (ACS)
DOI： 10.1021/acs.jcim.0c00551 　

ISSN： 1549-9596

eISSN： 1549-960X

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Enhanced conformational sampling, a genetic-algorithm-guided multidimensional virtual-system coupled molecular dynamics, can provide equilibrated conformational distributions of a receptor protein and a flexible ligand at room temperature. The distributions provide not only the most stable but also semistable complex structures and propose a ligand-receptor binding process. This method was applied to a system consisting of a receptor protein, 14-3-3ε, and a flexible peptide, phosphorylated myeloid leukemia factor 1 (pMLF1). The results present comprehensive binding pathways of pMLF1 to 14-3-3ε. We identified four thermodynamically stable clusters of MLF1 on the 14-3-3ε surface and free-energy barriers among some clusters. The most stable cluster includes two high-density spots connected by a narrow corridor. When pMLF1 passes the corridor, a salt-bridge relay (switching) related to the phosphorylated residue of pMLF1 occurs. Conformations in one high-density spot are similar to the experimentally determined complex structure. Three-dimensional distributions of residues in the intermolecular interface rationally explain the binding constant changes resulting from the alanine mutation experiment for the residues. We also performed a simulation of nonphosphorylated peptide and 14-3-3ε, which demonstrated that the complex structure was unstable, suggesting that phosphorylation of the peptide is crucially important for binding to 14-3-3ε.
Current State and Perspectives Related to the Polyethylene Terephthalate Hydrolases Available for Biorecycling Peer-reviewed

Fusako Kawai, Takeshi Kawabata, Masayuki Oda

ACS Sustainable Chemistry & Engineering　2020/06/05
Publisher: American Chemical Society (ACS)
DOI： 10.1021/acssuschemeng.0c01638 　

ISSN： 2168-0485

eISSN： 2168-0485
The Biological Structure Model Archive (BSM-Arc): an archive for in silico models and simulations Peer-reviewed

Gert-Jan Bekker, Takeshi Kawabata, Genji Kurisu

Biophysical Reviews　2020/02/05
Publisher: Springer Science and Business Media {LLC}
DOI： 10.1007/s12551-020-00632-5 　

ISSN： 1867-2469
Current knowledge on enzymatic PET degradation and its possible application to waste stream management and other fields. Peer-reviewed

Kawai F, Kawabata T, Oda M

Applied microbiology and biotechnology　103　(11)　4253-4268　2019/06

DOI： 10.1007/s00253-019-09717-y 　

ISSN： 0175-7598
Multimodal Structural Distribution of the p53 C-Terminal Domain upon Binding to S100B via a Generalized Ensemble Method: From Disorder to Extradisorder. Peer-reviewed

Iida S, Kawabata T, Kasahara K, Nakamura H, Higo J

Journal of chemical theory and computation　15　(4)　2597-2607　2019/04

DOI： 10.1021/acs.jctc.8b01042 　

ISSN： 1549-9618
Rigid Body Fitting of Atomic Models on Electron Density Map Using Gaussian Mixture Model Invited

Takeshi KAWABATA

Seibutsu Butsuri　59　(6)　320-323　2019
Publisher: Biophysical Society of Japan
DOI： 10.2142/biophys.59.320 　

ISSN： 0582-4052

eISSN： 1347-4219
Detection of cave pockets in large molecules: Spaces into which internal probes can enter, but external probes from outside cannot Peer-reviewed

Takeshi Kawabata

Biophysics and Physicobiology　16　(0)　391-406　2019
Publisher: Biophysical Society of Japan
DOI： 10.2142/biophysico.16.0_391 　

eISSN： 2189-4779
Gaussian-input Gaussian mixture model for representing density maps and atomic models Peer-reviewed

Takeshi Kawabata

Journal of Structural Biology　203　(1)　1-16　2018/07/01
Publisher: Academic Press Inc.
DOI： 10.1016/j.jsb.2018.03.002 　

ISSN： 1095-8657 1047-8477
統合失調症に強い関連を示した稀な遺伝子変異に基づく精神疾患の分子病態解明

木村大樹, 藤田幸, 川端猛, 森大輔, 岩山佳美, 岡久祐子, 池田匡志, 岩田仲生, 吉川武男, 山下俊英, 中村春木, 尾崎紀夫

先進医薬研究振興財団研究成果報告集　2017年度　80-81　2018/03
Publisher: (公財)先進医薬研究振興財団
ISSN： 2189-1303
Structural and mutational analysis of polyethylene terephthalate-hydrolyzing enzyme, cut190, based on three-dimensional docking structure with model compounds of polyethylene terephthalate

Takeshi Kawabata, Masayuki Oda, Nobutaka Numoto, Fusako Kawai

ACS Symposium Series　1310　63-75　2018
Publisher: American Chemical Society
DOI： 10.1021/bk-2018-1310.ch005 　

ISSN： 1947-5918 0097-6156
Rigid-Body Fitting of Atomic Models on 3D Density Maps of Electron Microscopy. Peer-reviewed

Kawabata T

Advances in experimental medicine and biology　1105　219-235　2018

DOI： 10.1007/978-981-13-2200-6_14 　

ISSN： 0065-2598
New tools and functions in data-out activities at Protein Data Bank Japan (PDBj) Peer-reviewed

Akira R. Kinjo, Gert-Jan Bekker, Hiroshi Wako, Shigeru Endo, Yuko Tsuchiya, Hiromu Sato, Hafumi Nishi, Kengo Kinoshita, Hirofumi Suzuki, Takeshi Kawabata, Masashi Yokochi, Takeshi Iwata, Naohiro Kobayashi, Toshimichi Fujiwara, Genji Kurisu, Haruki Nakamura

Protein Science　27　(1)　95-102　2017/09
Publisher: Wiley
DOI： 10.1002/pro.3273 　

ISSN： 0961-8368
Rare genetic variants in CX3CR1 and their contribution to the increased risk of schizophrenia and autism spectrum disorders Peer-reviewed

K Ishizuka, Y Fujita, T Kawabata, H Kimura, Y Iwayama, T Inada, Y Okahisa, J Egawa, M Usami, I Kushima, Y Uno, T Okada, M Ikeda, B Aleksic, D Mori, To Someya, T Yoshikawa, N Iwata, H Nakamura, T Yamashita, N Ozaki

Translational Psychiatry　7　(8)　e1184-e1184　2017/08
Publisher: Springer Science and Business Media LLC
DOI： 10.1038/tp.2017.173 　

eISSN： 2158-3188
A novel rare variant R292H in RTN4R affects growth cone formation and possibly contributes to schizophrenia susceptibility Peer-reviewed

H Kimura, Y Fujita, T Kawabata, K Ishizuka, C Wang, Y Iwayama, Y Okahisa, I Kushima, M Morikawa, Y Uno, T Okada, M Ikeda, T Inada, A Branko, D Mori, T Yoshikawa, N Iwata, H Nakamura, T Yamashita, N Ozaki

Translational Psychiatry　7　(8)　e1214-e1214　2017/08
Publisher: Springer Science and Business Media LLC
DOI： 10.1038/tp.2017.170 　

eISSN： 2158-3188
Mutational analysis of cutinase-like enzyme, Cut190, based on the 3D docking structure with model compounds of polyethylene terephthalate Peer-reviewed

Takeshi Kawabata, Masayuki Oda, Fusako Kawai

JOURNAL OF BIOSCIENCE AND BIOENGINEERING　124　(1)　28-35　2017/07

DOI： 10.1016/j.jbiosc.2017.02.007 　

ISSN： 1389-1723

eISSN： 1347-4421
HOMCOS: an updated server to search and model complex 3D structures Peer-reviewed

Takeshi Kawabata

Journal of Structural and Functional Genomics　17　(4)　83-99　2016/12/01
Publisher: Springer Netherland
DOI： 10.1007/s10969-016-9208-y 　

ISSN： 1570-0267 1345-711X
Toward the next step in G protein-coupled receptor research: a knowledge-driven analysis for the next potential targets in drug discovery Peer-reviewed

Koji Nagata, Yukie Katayama, Tomomi Sato, Yeondae Kwon, Takeshi Kawabata

Journal of Structural and Functional Genomics　17　(4)　111-133　2016/12/01
Publisher: Springer Netherland
DOI： 10.1007/s10969-016-9212-2 　

ISSN： 1570-0267 1345-711X
VaProS: a database-integration approach for protein/genome information retrieval Peer-reviewed

Takashi Gojobori, Kazuho Ikeo, Yukie Katayama, Takeshi Kawabata, Akira R. Kinjo, Kengo Kinoshita, Yeondae Kwon, Ohsuke Migita, Hisashi Mizutani, Masafumi Muraoka, Koji Nagata, Satoshi Omori, Hideaki Sugawara, Daichi Yamada, Kei Yura

Journal of Structural and Functional Genomics　17　(4)　69-81　2016/12/01
Publisher: Springer Netherland
DOI： 10.1007/s10969-016-9211-3 　

ISSN： 1570-0267 1345-711X
Homozygous inactivation of CHEK2 is linked to a familial case of multiple primary lung cancer with accompanying cancers in other organs. International-journal Peer-reviewed

Kukita Y, Okami J, Yoneda-Kato N, Nakamae I, Kawabata T, Higashiyama M, Kato J, Kodama K, Kato K

Cold Spring Harbor molecular case studies　2　(6)　a001032　2016/11

DOI： 10.1101/mcs.a001032 　

ISSN： 2373-2873

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In clinical practice, there are a number of cancer patients with clear family histories, but the patients lack mutations in known familial cancer syndrome genes. Recent advances in genomic technologies have enhanced the possibility of identifying causative genes in such cases. Two siblings, an elder sister and a younger brother, were found to have multiple primary lung cancers at the age of 60. The former subsequently developed breast cancer and had a history of uterine myoma. The latter had initially developed prostate cancer at the age of 59 and had a history of colon cancer. Single-nucleotide polymorphism (SNP) genotyping revealed that ∼10% of the genomes were homozygous in both patients. Exome sequencing revealed nonsynonymous mutations in five genes in the runs of homozygosity: CHEK2, FCGRT, INPP5J, MYO18B, and SFI1. Evolutionary conservation of primary protein structures suggested the functional importance of the CHEK2 mutation, p.R474C. This mutation altered the tertiary structure of CHK2 by disrupting the salt bridge between p.R474 and p.E394. No such structural changes were observed with the other mutated genes. Subsequent cell-based transfection analysis revealed that CHK2 p.R474C was unstable and scarcely activated. We concluded that the homozygous CHEK2 variant was contributory in this case of familial cancer. Although homozygous inactivation of CHEK2 in mice led to cancers in multiple organs, accumulation of additional human cases is needed to establish its pathogenic role in humans.
Gene expression and pathway analysis of CTNNB1 in cancer and stem cells Peer-reviewed

Shihori Tanabe, Takeshi Kawabata, Kazuhiko Aoyagi, Hiroshi Yokozaki, Hiroki Sasaki

WORLD JOURNAL OF STEM CELLS　8　(11)　384-395　2016/11

DOI： 10.4252/wjsc.v8.i11.384 　

ISSN： 1948-0210
Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures Peer-reviewed

Akira R. Kinjo, Gert-Jan Bekker, Hirofumi Suzuki, Yuko Tsuchiya, Takeshi Kawabata, Yasuyo Ikegawa, Haruki Nakamura

Nucleic Acids Research　45　(D1)　D282-D288　2016/10
Publisher: Oxford University Press ({OUP})
DOI： 10.1093/nar/gkw962 　

ISSN： 0305-1048
Omokage search: shape similarity search service for biomolecular structures in both the PDB and EMDB Peer-reviewed

Hirofumi Suzuki, Takeshi Kawabata, Haruki Nakamura

BIOINFORMATICS　32　(4)　619-620　2016/02

DOI： 10.1093/bioinformatics/btv614 　

ISSN： 1367-4803

eISSN： 1460-2059
Comparison of genetic structures and biochemical properties of tandem cutinase-type polyesterases from Thermobifida alba AHK119 Peer-reviewed

Uschara Thumarat, Takeshi Kawabata, Maho Nakajima, Hajime Nakajima, Akifumi Sugiyama, Kazufumi Yazaki, Tomoko Tada, Tomonori Waku, Naoki Tanaka, Fusako Kawai

JOURNAL OF BIOSCIENCE AND BIOENGINEERING　120　(5)　491-497　2015/11

DOI： 10.1016/j.jbiosc.2015.03.006 　

ISSN： 1389-1723

eISSN： 1347-4421
3D Flexible Alignment Using 2D Maximum Common Substructure: Dependence of Prediction Accuracy on Target-Reference Chemical Similarity Peer-reviewed

Takeshi Kawabata, Haruki Nakamura

JOURNAL OF CHEMICAL INFORMATION AND MODELING　54　(7)　1850-1863　2014/07

DOI： 10.1021/ci500006d 　

ISSN： 1549-9596

eISSN： 1549-960X
KCOMBU: A Program to Compare and Model Chemical Structures Invited

Takeshi KAWABATA

Seibutsu Butsuri　54　(3)　163-165　2014
Publisher: Biophysical Society of Japan
DOI： 10.2142/biophys.54.163 　

ISSN： 0582-4052

eISSN： 1347-4219
1P016 Superimposing density maps and atomic models of macromolecular complexes using Gaussian mixture model(01A. Protein:Structure,Poster)

Kawabata Takeshi, Suzuki Hirofumi, Kinjo Akira, Nakamura Haruki

Seibutsu Butsuri　53　(1)　S108　2013
Publisher: The Biophysical Society of Japan General Incorporated Association
DOI： 10.2142/biophys.53.S108_4 　
Comparison of Polyester-Degrading Cutinases from Genus Thermobifida Peer-reviewed

Fusako Kawai, Uschara Thumarat, Kengo Kitadokoro, Tomonori Waku, Tomoko Tada, Naoki Tanaka, Takeshi Kawabata

GREEN POLYMER CHEMISTRY: BIOCATALYSIS AND MATERIALS II　1144　111-120　2013

ISSN： 0097-6156
Catalytic Mechanism of Short Ethoxy Chain Nonylphenol Dehydrogenase Belonging to a Polyethylene Glycol Dehydrogenase Group in the GMC Oxidoreductase Family Peer-reviewed

Xin Liu, Takeshi Ohta, Takeshi Kawabata, Fusako Kawai

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES　14　(1)　1218-1231　2013/01

DOI： 10.3390/ijms14011218 　

ISSN： 1422-0067
LigandBox: A database for 3D structures of chemical compounds Peer-reviewed

Takeshi Kawabata, Yusuke Sugihara, Yoshifumi Fukunishi, Haruki Nakamura

Biophysics (Japan)　9　113-121　2013

DOI： 10.2142/biophysics.9.113 　

ISSN： 1349-2942
Biochemical and genetic analysis of a cutinase-type polyesterase from a thermophilic Thermobifida alba AHK119 Peer-reviewed

Uschara Thumarat, Ryota Nakamura, Takeshi Kawabata, Hideyuki Suzuki, Fusako Kawai

APPLIED MICROBIOLOGY AND BIOTECHNOLOGY　95　(2)　419-430　2012/07

DOI： 10.1007/s00253-011-3781-6 　

ISSN： 0175-7598
Book Review 2 Invited

Seibutsu Butsuri　52　(1)　054-055　2012
Publisher: Biophysical Society of Japan
DOI： 10.2142/biophys.52.054 　

ISSN： 0582-4052

eISSN： 1347-4219
Build-Up Algorithm for Atomic Correspondence between Chemical Structures Peer-reviewed

Takeshi Kawabata

JOURNAL OF CHEMICAL INFORMATION AND MODELING　51　(8)　1775-1787　2011/08

DOI： 10.1021/ci2001023 　

ISSN： 1549-9596
Detection of multiscale pockets on protein surfaces using mathematical morphology Peer-reviewed

Takeshi Kawabata

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS　78　(5)　1195-1211　2010/04

DOI： 10.1002/prot.22639 　

ISSN： 0887-3585
Multiple Subunit Fitting into a Low-Resolution Density Map of a Macromolecular Complex Using a Gaussian Mixture Model Peer-reviewed

Takeshi Kawabata

BIOPHYSICAL JOURNAL　95　(10)　4643-4658　2008/11

DOI： 10.1529/biophysj.108.137125 　

ISSN： 0006-3495
HOMCOS: a server to predict interacting protein pairs and interacting sites by homology modeling of complex structures Peer-reviewed

Naoshi Fukuhara, Takeshi Kawabata

NUCLEIC ACIDS RESEARCH　36　(Web Server issue)　W185-W189　2008/07

DOI： 10.1093/nar/gkn218 　

ISSN： 0305-1048
Detection of pockets on protein surfaces using small and large probe spheres to find putative ligand binding sites Peer-reviewed

Takeshi Kawabata, Nobuhiro Go

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS　68　(2)　516-529　2007/08

DOI： 10.1002/prot.21283 　

ISSN： 0887-3585
1P253 Multiple protein docking guided by low-resolution image of complex using Gaussian mixture model under the symmetric constraint(Bioinformatics-structural genomics,Poster Presentations)

Kawabata Takeshi, Yura Kei

Seibutsu Butsuri　47　S86　2007
Publisher: The Biophysical Society of Japan General Incorporated Association
DOI： 10.2142/biophys.47.S86_4 　
1P243 Prediction of the phenotypic effects of nsSNPs focusing accessibility, pocketness and site-specific probabilities of substituted residues(Bioinformatics-structural genomics,Poster Presentations)

Yoshii Yuuki, Kawabata Takeshi

Seibutsu Butsuri　47　S84　2007
Publisher: The Biophysical Society of Japan General Incorporated Association
DOI： 10.2142/biophys.47.S84_2 　
Prediction of interacting proteins from homology-modeled complex structures using sequence and structure scores Peer-reviewed

Naoshi Fukuhara, Nobuhiro Go, Takeshi Kawabata

Biophysics　3　13-26　2007

DOI： 10.2142/biophysics.3.13 　

ISSN： 1349-2942
Double-stranded DNA binding, an unusual property of DNA polymerase epsilon, promotes epigenetic silencing in Saccharomyces cerevisiae Peer-reviewed

Toshiaki Tsubotao, Rie Tajima, Kunitomo Ode, Hajime Kubota, Naoshi Fukuhara, Takeshi Kawabata, Satoko Maki, Hisaji Maki

JOURNAL OF BIOLOGICAL CHEMISTRY　281　(43)　32898-32908　2006/10

DOI： 10.1074/jbc.M606637200 　

ISSN： 0021-9258
Analysis of amino acid residues involved in catalysis of polyethylene glycol dehydrogenase from Sphingopyxis terrae, using three-dimensional molecular modeling-based kinetic characterization of mutants Peer-reviewed

T Ohta, T Kawabata, K Nishikawa, A Tani, K Kimbara, F Kawai

APPLIED AND ENVIRONMENTAL MICROBIOLOGY　72　(6)　4388-4396　2006/06

DOI： 10.1128/AEM.02174-05 　

ISSN： 0099-2240

eISSN： 1098-5336
1P194 Multiple protein docking guided by low-resolution image of complex using Gaussian mixture model(6. Macromolecular assembly,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)

Kawabata Takeshi, Yura Kei

Seibutsu Butsuri　46　(2)　S195　2006
Publisher: The Biophysical Society of Japan General Incorporated Association
DOI： 10.2142/biophys.46.S195_2 　
1P484 Predicted Protein-Protein Interaction Networks based on Homology-Modeled Complex Structures(23. Bioinformatics, genomics and proteomics (I),Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)

Fukuhara Naoshi, Kawabata Takeshi, Go Nobuhiro

Seibutsu Butsuri　46　(2)　S267　2006
Publisher: The Biophysical Society of Japan General Incorporated Association
DOI： 10.2142/biophys.46.S267_4 　
The first crystal structure of an archaeal helical repeat protein Peer-reviewed

K Yoneda, H Sakuraba, H Tsuge, N Katunuma, S Kuramitsu, T Kawabata, T Ohshima

ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY AND CRYSTALLIZATION COMMUNICATIONS　61　(Pt 7)　636-639　2005/07

DOI： 10.1107/S1744309105019263 　

ISSN： 1744-3091
How to Use MATRAS Server? Invited

Takeshi KAWABATA

Seibutsu Butsuri　45　(1)　41-44　2005
Publisher: Biophysical Society of Japan
DOI： 10.2142/biophys.45.41 　

ISSN： 0582-4052

eISSN： 1347-4219
1P291 A knowledge-based trial to gain information for atomic resolution structures of supra-molecules out of their images by electron microscopy

Yura K., Ishida H., Iwasaki K., Kawabata T., Tsutsumi Y., Matsumoto A., Mayanagi K.

Seibutsu Butsuri　45　S104　2005
Publisher: The Biophysical Society of Japan General Incorporated Association
DOI： 10.2142/biophys.45.S104_3 　
1P284 Prediction of protein-protein interaction using statistical potential

Fukuhara N., Kawabata T., Go N.

Seibutsu Butsuri　45　S102　2005
Publisher: The Biophysical Society of Japan General Incorporated Association
DOI： 10.2142/biophys.45.S102_4 　
3P006 Fast Fitting Calculation of Low Resolution Protein Structures using Gaussian Mixture Model

Kawabata T., Yuta K., Go N.

Seibutsu Butsuri　45　S205　2005
Publisher: The Biophysical Society of Japan General Incorporated Association
DOI： 10.2142/biophys.45.S205_2 　
Electrostatic potential of nucleotide-free protein is sufficient for discrimination between adenine and guanine-specific binding sites Peer-reviewed

G Basu, D Sivanesan, T Kawabata, N Go

JOURNAL OF MOLECULAR BIOLOGY　342　(3)　1053-1066　2004/09

DOI： 10.1016/j.jmb.2004.07.047 　

ISSN： 0022-2836

eISSN： 1089-8638
Filtering remote homologues using predicted structural information Peer-reviewed

K Uehara, T Kawabata, N Go

PROTEIN ENGINEERING DESIGN & SELECTION　17　(7)　565-570　2004/07

DOI： 10.1093/protein/gzh065 　

ISSN： 1741-0126
Finding evolutionary relations beyond superfamilies: Fold-based superfamilies Peer-reviewed

K Matsuda, T Nishioka, K Kinoshita, T Kawabata, N Go

PROTEIN SCIENCE　12　(10)　2239-2251　2003/10

DOI： 10.1110/ps0383603 　

ISSN： 0961-8368
Novel types of two-domain multi-copper oxidases: possible missing links in the evolution Peer-reviewed

K Nakamura, T Kawabata, K Yura, N Go

FEBS LETTERS　553　(3)　239-244　2003/10

DOI： 10.1016/S0014-5793(03)01000-7 　

ISSN： 0014-5793
MATRAS: a program for protein 3D structure comparison Peer-reviewed

T Kawabata

NUCLEIC ACIDS RESEARCH　31　(13)　3367-3369　2003/07

DOI： 10.1093/nar/gkg581 　

ISSN： 0305-1048
On the Accuracy of Transmembrane Segment Prediction of Helical Integral Membrane Proteins

Tanimoto Shin, Basu Gautam, Kawabata Takeshi, Go Nobuhiro

GI　14　557-558　2003
Publisher: Japanese Society for Bioinformatics
DOI： 10.11234/gi1990.14.557 　

ISSN： 0919-9454
Development of a method for Prcotein Remote Homologue Detection Using Secondary Structure Prediction

Uehara K., Kawabata T., Go N.

Seibutsu Butsuri　43　S212　2003
Publisher: The Biophysical Society of Japan General Incorporated Association
DOI： 10.2142/biophys.43.S212_4 　
Prediction of protein-protein interaction sites on the basis of the distribution of the surface residues.

Fukuhara N., Kawabata T., Go N.

Seibutsu Butsuri　43　S212　2003
Publisher: The Biophysical Society of Japan General Incorporated Association
DOI： 10.2142/biophys.43.S212_3 　
A systematic investigation identifies a significant number of probable pseudogenes in the Escherichia coli genome Peer-reviewed

K Homma, S Fukuchi, T Kawabata, M Ota, K Nishikawa

GENE　294　(1-2)　25-33　2002/07

DOI： 10.1016/s0378-1119(02)00794-1 　

ISSN： 0378-1119
Solution structure of the fibronectin type III domain from Bacillus circulans WL-12 chitinase A1 Peer-reviewed

JG Jee, T Ikegami, M Hashimoto, T Kawabata, M Ikeguchi, T Watanabe, M Shirakawa

JOURNAL OF BIOLOGICAL CHEMISTRY　277　(2)　1388-1397　2002/01

DOI： 10.1074/jbc.M109726200 　

ISSN： 0021-9258
GTOP: a database of protein structures predicted from genome sequences Peer-reviewed

T Kawabata, S Fukuchi, K Homma, M Ota, J Araki, T Ito, N Ichiyoshi, K Nishikawa

NUCLEIC ACIDS RESEARCH　30　(1)　294-298　2002/01

DOI： 10.1093/nar/30.1.294 　

ISSN： 0305-1048
Structural/functional assignment of unknown bacteriophage T4 proteins by iterative database searches Peer-reviewed

T Kawabata, F Arisaka, K Nishikawa

GENE　259　(1-2)　223-233　2000/12

ISSN： 0378-1119
Protein structure comparison using the Markov transition model of evolution Peer-reviewed

T Kawabata, K Nishikawa

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS　41　(1)　108-122　2000/10

ISSN： 0887-3585

eISSN： 1097-0134
Report on CASP3. Invited

Takeshi KAWABATA, Ken NISHIKAWA

Seibutsu Butsuri　40　(1)　52-56　2000
Publisher: Biophysical Society of Japan
DOI： 10.2142/biophys.40.52 　

ISSN： 0582-4052

eISSN： 1347-4219
Cooperative approach for the protein fold recognition Peer-reviewed

M Ota, T Kawabata, AR Kinjo, K Nishikawa

PROTEINS-STRUCTURE FUNCTION AND GENETICS　126-132　1999

ISSN： 0887-3585
The protein mutant database Peer-reviewed

T Kawabata, M Ota, K Nishikawa

NUCLEIC ACIDS RESEARCH　27　(1)　355-357　1999/01

ISSN： 0305-1048

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Misc. 14

Remote homology detection through 3D structural comparison of tertiary predicted structures by AlphaFold2

Takeshi Kawabata, Kengo Kinoshita

2024/06
AlphaFoldDBの予測立体構造を用いた遠縁のホモログタンパク質の認識

川端猛, 木下賢吾

日本蛋白質科学会年会プログラム・要旨集　23rd (CD-ROM)　2023
Biological Structure Model Archive: An archive for computationally obtained data

BEKKER Gert-Jan, KAWABATA Takeshi, KURISU Genji

生物物理(Web)　59　(Supplement 1-2)　2019

ISSN： 1347-4219
統合失調症に強い関連を示した稀な遺伝子変異に基づく精神疾患の分子病態解明

木村大樹, 藤田幸, 川端猛, 森大輔, 岩山佳美, 岡久祐子, 池田匡志, 岩田仲生, 吉川武男, 山下俊英, 中村春木, 尾崎紀夫

先進医薬研究振興財団研究成果報告集　2017年度　80-81　2018/03
Publisher: (公財)先進医薬研究振興財団
ISSN： 2189-1303
統合失調症発症に強い影響を及ぼす、頻度の低い稀な遺伝子変異を22q11.2欠失領域に存在するミエリン関連遺伝子のRTN4Rに同定した

木村大樹, 藤田幸, 川端猛, 石塚佳奈子, Wang Chenyao, 岩山佳美, 岡久祐子, 久島周, 宇野洋太, 岡田俊, 森川真子, 森大輔, 池田匡志, 稲田俊也, Aleksic Branko, 吉川武男, 岩田仲生, 中村春木, 山下俊英, 尾崎紀夫

日本生物学的精神医学会・日本神経精神薬理学会合同年会プログラム・抄録集　39回・47回　190-190　2017/09
Publisher: 日本生物学的精神医学会・日本神経精神薬理学会
Protein Data Bank Japan (PDBj): updated semantic web services and tools for large structures

A. R. Kinjo, G-J. Bekker, H. Suzuki, Y. Tsuchiya, T. Kawabata, Y. Ikegawa, G. Kurisu, H. Nakamura

EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS　46　S274-S274　2017/07

ISSN： 0175-7571

eISSN： 1432-1017
統合失調症発症に強い影響を及ぼす、頻度の低い稀な遺伝子変異を22q11.2欠失領域に存在するミエリン関連遺伝子のRTN4Rに同定した

木村大樹, 尾崎紀夫, 藤田幸, 川端猛, 石塚佳奈子, Wang Chenyao, 岩山佳美, 岡久祐子, 久島周, 森川真子, 宇野洋太, 岡田俊, 森大輔, 池田匡志, 稲田俊也, Aleksic Branko, 吉川武男, 岩田仲生, 中村春木, 山下俊英

精神神経学雑誌　(2017特別号)　S622-S622　2017/06
Publisher: (公社)日本精神神経学会
ISSN： 0033-2658
Searching and viewing hybrid structure data

Hirofumi Suzuki, Gert-Jan Bekker, Takeshi Kawabata, Genji Kurisu, Haruki Nakamura

ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES　73　C974-C974　2017

DOI： 10.1107/S2053273317086004 　

ISSN： 2053-2733
Omokage Search and Gmfit: Shape Similarity Search and Superposition among Models and Maps

Takeshi Kawabata, Hirofumi Suzuki, Haruki Nakamura

BIOPHYSICAL JOURNAL　110　(3)　157A-157A　2016/02

ISSN： 0006-3495

eISSN： 1542-0086
Web based services for multiscale structure data in EMDB, PDB and SASBDB

SUZUKI Hirofumi, SUZUKI Hirofumi, KAWABATA Takeshi, BEKKER Gert-Jan, BEKKER Gert-Jan, NAKAMURA Haruki, NAKAMURA Haruki

生物物理(Web)　56　(Supplement 1-2)　2016

ISSN： 1347-4219
A Comparison of 3D Conformations of Endothelin-1 Analogs to Find the Pharmacophore Model Required for Endothelin Receptor Ligand Activity

M. A. Benson, Takeshi Kawabata, Narutoshi Kamiya, Haruki Nakamura

BIOPHYSICAL JOURNAL　106　(2)　479A-479A　2014/01

ISSN： 0006-3495

eISSN： 1542-0086
Homcos : A Server to Search and Model 3D Structures of Protein-Protein and Compound-Protein Complexes

Takeshi Kawabata, Haruki Nakamura, Akira Kinjo

BIOPHYSICAL JOURNAL　106　(2)　207A-207A　2014/01

ISSN： 0006-3495

eISSN： 1542-0086
Comparison of two polyester-degrading enzymes from Thermobifida alba AHK119

Fusako Kawai, Uschara Thumarat, Kengo Kitadokoro, Naoki Tanaka, Takeshi Kawabata

ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY　244　2012/08

ISSN： 0065-7727
Electrostatic discrimination between adenine- and guanine-specific binding sites in proteins

G Basu, D Sivanesan, T Kawabata, N Go

PROTEIN SCIENCE　13　75-75　2004/08

ISSN： 0961-8368

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Books and Other Publications 6

実験医学増刊 Vol.40 No.17 バイオDBとウェブツールラボで使える最新70選〜知る・学ぶ・使う、バイオDX時代の羅針盤

小野, 浩雅

羊土社　2022/10/24

ISBN: 4758104069
バイオインフォマティクス入門第2版

日本バイオインフォマティクス学会

慶應義塾大学出版会　2021/12/17

ISBN: 4766427912
よくわかるバイオインフォマティクス入門 (KS生命科学専門書)

岩部直之, 川端猛, 浜田道昭, 門田幸二, 須山幹太, 光山統泰, 黒川顕, 森宙史, 東光一, 吉沢明康, 片山俊明

講談社　2018/11/19

ISBN: 4065138213
見てわかる構造生命科学: 生命科学研究へのタンパク質構造の利用

中村, 春木, 川端, 猛, 鷹野, 優, 鈴木, 博文, 緒方, 一博, 椎名, 政昭, 笠原, 浩太, 寒川, 剛, 大島, 勘二, 神谷, 成敏

化学同人　2014/04/03

ISBN: 4759815775
タンパク質の立体構造入門――基礎から構造バイオインフォマティクスへ (KS生命科学専門書)

藤, 博幸, 太田, 元規, 川端, 猛, 木下, 賢吾, 白井, 剛, 諏訪, 牧子, 高田, 彰二, 高橋, 聡, 廣明, 秀一, 真柳, 浩太, 倭, 剛久, 由良, 敬

講談社　2010/11/25

ISBN: 4061538810
はじめてのバイオインフォマティクス (KS生命科学専門書)

藤, 博幸, 講談社サイエンティフィク

講談社　2006/12/18

ISBN: 4061538624

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Research Projects 8

Prediction of Interacting Molecules and Their 3D Structures using Structure Search and Graph Neural Networks

Offer Organization: Japan Society for the Promotion of Science

System: Grants-in-Aid for Scientific Research

Category: Grant-in-Aid for Scientific Research (C)

Institution: Tohoku University

2024/04 - 2027/03
Multiscale atomic modeling based on electron microscopy 3D map using Gaussian mixture model

Kawabata Takeshi

Offer Organization: Japan Society for the Promotion of Science

System: Grants-in-Aid for Scientific Research

Category: Grant-in-Aid for Scientific Research (C)

Institution: Osaka University

2017/04/01 - 2021/03/31

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We have developed several atomic modeling methods based on Cryo-EM 3D density map with near-atomic resolution using Gaussian mixture model (GMM). In order to convert to a map (or an atomic model) into a GMM with the same size, “Gaussian-input GMM” and “down-sampling GMM” methods have been invented. We also developed a new algorithm “cave pocket” to detect an internal hollow space in a large macromolecular complex using mathematical morphology. The method “masked segmentation & fitting” has been developed to fit multiple atomic models of subunits into a local region of 3D map.
Comparison and superposition of low-resolution density maps and atomic models using Gaussian mixture model

KAWABATA TAKESHI, SUZUKI HIROFUMI

Offer Organization: Japan Society for the Promotion of Science

System: Grants-in-Aid for Scientific Research

Category: Grant-in-Aid for Scientific Research (C)

Institution: Osaka University

2014/04/01 - 2017/03/31

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3D density maps by electron microscopy have important information about biomolecular structures. To make a full use of these maps, we developed a WEB server “Omokage search” to search the global shape similarity of biological macromolecules in databases for 3D density maps and atomic models. The server searches using the distance-based profiles from the 3D points of the maps and models. It also performs 3D superimpositions using the Gaussian mixture model (GMM), for approximating shapes of the maps and the models. The new algorithm “Gaussian-input GMM” was developed for converting into GMMs more robustly and rapidly. We started to develop the methods for multiple subunit fitting and alpha-helix detection.
A searching method for interacting chemical compounds for target proteins using 3D structures of compound-protein complexes

KAWABATA Takeshi

Offer Organization: Japan Society for the Promotion of Science

System: Grants-in-Aid for Scientific Research

Category: Grant-in-Aid for Scientific Research (C)

2010 - 2012

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We developed the program kcombu to calculate one-to-one atomic correspondences from 2D structures of chemical compounds. The method is based on the classical concept, maximum common substructure (MCS). Our method employs the fast heuristic “build-up” algorithm, and calculates topologoically-constrained disconnected MCS (TD-MCS) in addition to conventional connected and disconnected MCS. Based on this program, we developed a template-based structural prediction method of chemical compounds. We also researched common and specific 3D features of chemical compounds, which bind to proteins of the same family.
Analysis of geometric shapes of binding sites on protein-ligand complex for prediction of molecular interactions

KAWABATA Takeshi

Offer Organization: Japan Society for the Promotion of Science

System: Grants-in-Aid for Scientific Research

Category: Grant-in-Aid for Scientific Research (C)

Institution: Nara Institute of Science and Technology

2007 - 2008
タンパク質立体構造データベースに基づく分子間相互作用の解析

川端猛

Offer Organization: 日本学術振興会

System: 科学研究費助成事業

Category: 特定領域研究

Institution: 奈良先端科学技術大学院大学

2004 - 2004

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本研究は、豊富なタンパク質立体構造データベースを生かして、タンパク質間およびタンパク質-低分子間の結合(相互作用)を理解し、相互作用が未知のタンパク質について立体構造からその機能を予測することを最終目的とする。本年度は既知の複合体の立体構造データから相互作用部位の幾何学的特徴解析と蛋白質複合体のホモロジーモデリングを中心に行った。幾何学的特徴として凹形状を検出するアルゴリズムの開発を進めた。このアルゴリズムはまず小さなプローブ球と大きなプローブ球を蛋白質表面に多数置き、大きなプローブ球が接触できない小さなプローブ球の集合をポケットと定義した。プローブ球は蛋白質の3つの原子と接するように置く。今年度はプローブ生成の方法に改良を加え、計算時間がプローブ球の大きさに依存しない高速なアルゴリズムを開発した。検出された凹部位は実際の低分子結合部位と有意な相関があった。この成果は現在、論文準備中である。また、蛋白質間相互作用については、単純な幾何特徴だけでは予測は難しいため、複合体のホモロジーモデリングの可能性を模索した。まず、相互作用が進化的にどの程度保存するか検討したところ、ヘテロ複合体は同一残基率40%程度であれば比較的高い精度で予測できることがわかった。ホモ複合体は結晶のコンタクトの影響もあり、より不安定な予測になることがわかった。現在、これらの知見を酵母の全蛋白質に適用し、複合体をモデリングから新規の相互作用の予測することを試みている。また、相互作用以外に、基本的なホモロジーモデリングのフォールド認識の過程を2次構造予測を用いて感度を上げる試みも行った。この成果はProtein Engineering Design and Selection誌に出版された。また、構造比較サーバMATRASの維持作業も継続して行い、その紹介記事が「生物物理」誌に出版された。
立体構造比較によるタンパク質機能解析用データベースの開発

川端猛

Offer Organization: 日本学術振興会

System: 科学研究費助成事業

Category: 特定領域研究

Institution: 奈良先端科学技術大学院大学

2003 - 2003

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本研究の目的は、膨大なタンパク質の立体構造の情報をその分子機能の理解や推定に役立てるような手法とデータベースを開発することである。研究代表者は昨年度から立体構造比較サーバMATRASの開発を進めており、今年度も一層の機能の拡充を行った。立体構造比較は、構造から機能を推定するための最も基本的な方法であり、特に構造ゲノム科学の枠組みにおいて構造比較サーバを維持することの重要性は高い。今年度、開発したMATRASサーバの詳細をNucleic Acids Research誌に発表した結果、構造比較サーバの一つとして国際的にも認知されつつあり、現在、国内外から多くの検索依頼がある。さらに今年度は、構造から分子機能を理解するための次の3つの研究開発を行った。一つは、構造未知のアミノ酸配列から立体構造予測を行う方法の整備である。MATRASに配列比較の機能を追加したほか、2次構造予測を利用したPSI-BLASTの改良についても研究を行った。もう一つは、タンパク質間相互作用の相互作用サイトの予測の試みである。複合体の立体構造を決定することは一般に困難であるため、単量体の立体構造からその相互作用を予測する試みは重要である。まず、既知の複合体の相互作用サイトのアミノ酸分布の統計からシンプルなスコアを導出し、それを用いた単量体の相互作用サイトの予測法を行った。最後に、タンパク質表面のポケット部を認識するためのアルゴリズムの開発を行った。低分子を結合するタンパク質表面の多くは凹状のポケット型をしており、こうしたポケットを自動的に認識するプログラムは、低分子結合部位を推定する際に有用であると考えている。今後は、これら開発中の手法をより改良し、最終的にはMATRASサーバに統合して、機能推定のためのより高機能のサーバ・データベースを作成しようと考えている。
立体構造を中心とした統合タンパク質データベースの開発

川端猛

Offer Organization: 日本学術振興会

System: 科学研究費助成事業

Category: 特定領域研究

Institution: 奈良先端科学技術大学院大学

2002 - 2002

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本研究は、タンパク質の立体構造のデータを比較・分類し、さらにそれに関する配列データ等をリンクすることで、統合された有効なデータベースを作成することを目的とした。本年度は、まず、申請者が以前に開発した立体構造比較プログラム"Matras"を用いた立体構造比較をするWEBサーバ(http://biunit.aist-nara.ac.jp/Matras/)を開設・維持する作業を中心に行なった。これはユーザーが立体構造のIDを入力、あるいは原子座標をアップロードすることで、ペアワイズ・マルチプルの立体構造比較、さらには構造既知のライブラリに対する類似構造検索を行なうことができるサーバである。ペアワイズ、マルチプルの構造比較ではリアルタイムに結果が返答される。構造ライブラリ検索は20〜30分の計算時間がかかるため電子メールで結果を送信する形式を採用している。対象の構造ライブラリは週に一度更新される。このサーバは昨年夏に一般公開され、現在では国内外から検索依頼が来るようになっている。こういった立体構造比較サーバは欧米では既にいくつか存在するが、国内では、我々の知る限り、唯一の実働している比較サーバであり、その存在価値は高いと信じている。さらに、一般の生物学者からの要望を受けてアミノ酸配列からの立体構造検索サービスの機能も追加した。このサーバについては"Nucleic Acids Resarch"誌に投稿し審査中である。この立体構造比較Webサーバを中心として、様々な情報を取り込んでいくことで、より有用な統合データベースサーバを開発していくことを計画している。

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Teaching Experience 1

構造バイオインフォマティクス基礎　東京大学大学院農学生命科学研究科

Works 5

HOMCOS : A server for searching and modeling protein complexes (https://homcos.pdbj.org)

Takeshi Kawabata

2016/08 - Present

Type: Web Service
gmfit : a program for fitting atomic models on 3D EM map (https://pdbj.org/gmfit)

Takeshi Kawabata

2013 - Present

Type: Web Service
KCOMBU : A chemical structure comparison (https://pdbj.org/kcombu)

Takeshi Kawabata

2011/08 - Present

Type: Web Service
GHECOM : Detection of pockets on protein surface (https://pdbj.org/ghecom)

Takeshi Kawabata

2010 - Present

Type: Web Service
MATRAS: a server for protein structure comparison ( https://pdbj.org/matras/ )

Takeshi Kawabata

2003/07/01 - Present

Type: Web Service