Last Modified : 2022/03/26
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Publications
[Go back to the page of Takeshi Kawabata]
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Wang C, Horigane SI, Wakamori M, Ueda S, Kawabata T, Fujii H, Kushima I, Kimura H, Ishizuka K, Nakamura Y, Iwayama Y, Ikeda M, Iwata N, Okada T, Aleksic B, Mori D, Yoshida T, Bito H, Yoshikawa T, Takemoto-Kimura S, Ozaki N. Identification of ultra-rare disruptive variants in voltage-gated calcium channel-encoding genes in Japanese samples of schizophrenia and autism spectrum disorder. Transl Psychiatry. 2022 Feb 26;12(1):84. doi: 10.1038/s41398-022-01851-y. PMID: 35220405; PMCID: PMC8882172.
- Bekker GJ, Yokochi M, Suzuki H, Ikegawa Y, Iwata T, Kudou T, Yura K, Fujiwara T, Kawabata T, Kurisu G. Protein Data Bank Japan: Celebrating our 20th anniversary during a global pandemic as the Asian hub of three dimensional macromolecular structural data. Protein Sci. 2022 Jan;31(1):173-186. doi: 10.1002/pro.4211. Epub 2021 Oct 27. PMID: 34664328; PMCID: PMC8740847.
- Hayami T, Kamiya N, Kasahara K, Kawabata T, Kurita J, Fukunishi Y, Nishimura Y, Nakamura H,Higo J.
Difference of binding modes among three ligands to a receptor mSin3B corresponding to their inhibitory activities
Scientific Reports volume 11, Article number: 6178 (2021)
[doi: 10.1038/s41598-021-85612-9]
[PubMed]
[BSM-Arc]
- Ishizuka K, Yoshida T, Kawabata T, Imai A, Mori H, Kimura H, Inada T, Okahisa Y, Egawa J, Usami M, Kushima I, Morikawa M, Okada T, Ikeda M, Branko A, Mori D, Someya T, Iwata N, Ozaki N. (2020)
Functional characterization of rare NRXN1 variants identified in autism spectrum disorders and schizophrenia.
J Neurodev Disord. 2020 12:25.
[doi: 10.1186/s11689-020-09325-2],
[PubMed]
[BSM-Arc]
- Higo J, Kawabata T, Kusaka A, Kasahara K, Kamiya N, Fukuda I, Mori K, Hata Y, Fukunishi Y, Nakamura H. (2020)
Molecular Interaction Mechanism of a 14-3-3 Protein with a Phosphorylated Peptide Elucidated by Enhanced Conformational Sampling.
J Chem Inf Model. 2020,60:4867-4880. doi: 10.1021/acs.jcim.0c00551.
[doi: 10.1021/acs.jcim.0c00551
[PubMed]
[BSM-Arc]
- Gert-Jan Bekker G, Kawabata T, Kurisu G. (2020)
The Biological Structure Model Archive (BSM-Arc): an archive for in silico models and simulations
Biophys Rev . 2020 Apr;12(2):371-375.
doi: 10.1007/s12551-020-00632-5.
[doi: 10.1007/s12551-020-00632-5]
[PubMed]
- Iida S, Kawabata T, Kasahara K, Nakamura H, Higo J. (2019)
Multimodal Structural Distribution of the p53 C-Terminal Domain upon Binding to S100B via a Generalized Ensemble Method: From Disorder to Extradisorder. J Chem Theory Comput. 2019 Apr 9;15(4):2597-2607.
[doi: 10.1021/acs.jctc.8b01042]
[PubMed]
- Kawabata T. (2019) Detection of cave pockets in large molecules: Spaces into which internal probes can enter, but external probes from outside cannot.
Biophysics and Physicobiology,16,391-406, 2019. [Publisher]
- Kawabata T. (2018)
Gaussian-input Gaussian mixture model for representing density maps and atomic models.
J Struct Biol. 203:1-16, 2018
[PubMed]
[Publisher]
- Kinjo AR, Bekker GJ, Wako H, Endo S, Tsuchiya Y, Sato H, Nishi H, Kinoshita K, Suzuki H, Kawabata T, Yokochi M, Iwata T, Kobayashi N, Fujiwara T, Kurisu G, Nakamura H.(2017)
New tools and functions in data-out activities at Protein Data Bank Japan (PDBj).
Protein Sci. 2018 27, 95-102. doi: 10.1002/pro.3273. Epub 2017 Sep 18.
[PubMed]
- Kimura H, Fujita Y, Kawabata T, Ishizuka K, Wang C, Iwayama Y, Okahisa Y, Kushima I, Morikawa M, Uno Y, Okada T, Ikeda M, Inada T, Branko A, Mori D, Yoshikawa T, Iwata N, Nakamura H, Yamashita T, Ozaki N.(2017) A novel rare variant R292H in RTN4R affects growth cone formation and possibly contributes to schizophrenia susceptibility. Transl Psychiatry, 7, e1214. doi: 10.1038/tp.2017.170, 2017
[PubMed]
[BSM-Arc]
- Ishizuka K, Fujita Y, Kawabata T, Kimura H, Iwayama Y, Inada T, Okahisa Y, Egawa J, Usami M, Kushima I, Uno Y, Okada T, Ikeda M, Aleksic B, Mori D, Someya T, Yoshikawa T, Iwata N, Nakamura H, Yamashita T, Ozaki N.(2017) Rare genetic variants in CX3CR1 and their contribution to the increased risk of schizophrenia and autism spectrum disorders. Transl Psychiatry, 7, e1184. doi: 10.1038/tp.2017.173, 2017
[PubMed]
[BSM-Arc]
- Kawabata T, Oda M, Kawai F. (2017) Mutational analysis of cutinase-like enzyme, Cut190, based on the 3D docking structure with model compounds of polyethylene terephthalate. Journal of Bioscience and Bioengineering, 124:28-35, 2017
[PubMed]
[BSM-Arc]
- Kukita Y, Okami J, Yoneda-Kato N, Nakamae I, Kawabata T, Higashiyama M, Kato J, Kodama K, Kato K,(2016) Homozygous inactivation of CHEK2 is linked to a familial case of multiple primary lung cancer with accompanying cancers in other organs. Molecular Case Studies, 2, a001032, 2016.
[PubMed]
- Kinjo AR, Bekker, GJ, Suzuki H, Tsuchiya Y, Kawabata T, Ikegawa Y, Nakamura H, (2017)Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures. Nucleic Acids Research, 45(D1):D282-D288, 2017
[PubMed]
- Gokobori T, Ikeo K, Katayama Y, Kawabata T, Kinjo AR, Kinoshita K, Kwon Y, Migita O, Mizutani H, Muraoka M, Nagata K, Omori S, Sugawara H, Yamada D, Yura K. (2016) VaProS: a database-integration approach for protein/genome information retrieval. J. Struct. Funct. Genomics. 17:69-81, 2016
[PubMed]
[Publisher]
- Nagata K, Katayama Y, Sato T, Kwon Y, Kawabata T.(2016) Toward the next step in G protein-coupled receptor research: a knowledge-driven analysis for the next potential targets in drug discovery. J. Struct. Funct. Genomics. 17:111-133, 2016
[PubMed]
[Publisher]
- Kawabata T. (2016) HOMCOS: an update server to search and model complex 3D structures. J.Struct.Funct.Gennomics.
17, 83-99. [PubMed] [Publisher]
[Link to HOMCOS server]
- Suzuki H, Kawabata T, Nakamura H. (2016)
Omokage search: shape similarity search service for biomolecular structures in both the PDB and EMDB. Bioinformatics 32, 619-20.
[PubMed]
[Bioinformatics]
[Link to Omokage search page]
- Kawabata T., Nakamura,H. (2014).
3D flexible alignment using 2D maximum common substructure: dependence of prediction accuracy on target-reference chemical similarity.
J.Chem.Info.Model.,54, 1850-1863.
[PubMed]
[Link to KCOMBU server]
- Kawabata,T., Sugihara, Y., Fukunishi, Y., Nakamura, H. (2013). LigandBox : a database for 3D structures of chemical compounds. BIOPHYSICS,9,113-121
[PubMed]
[Link to LigandBox server]
- Kawabata T. (2011).
Build-up algorithm for atomic correspondence between chemical structures.
J.Chem.Info.Model., 51, 1775-1787.
[PubMed]
[Link to KCOMBU server]
- Kawabata T. (2010).
Detection of multi-scale pockets on protein surfaces using mathematical morphology.
Proteins, 78,1195-211.
[PubMed]
[Link to GHECOM server]
- Kawabata T. (2008).
Multiple subunit fitting into a low-resolution density map of a macromolecular complex using Gaussian mixture model.
Biophysical Journal, 95,4643-4658.
[PubMed]
- Fukuhara N., Kawabata T. (2008).
HOMCOS: A server to predict interacting protein pairs and interacting sites by homology modeling of complex structures.
Nucleic Acids Research, 36, Web server issue, W185-W189.
[PubMed]
[Nucl.Acids Res.]
- Fukuhara N., Go N., Kawabata T. (2007).
Prediction of Interacting Proteins from Homology-modeled Complex
Structures Using Sequence and Structure Scores,
BIOPHYSICS, Vol.3, 13-26
[PubMed]
[J-Stage]
- Kawabata T, Go N. (2007)
Detection of pockets on protein surfaces using small and large probe spheres to find putative ligand binding sites. Proteins, 68,516-529.
[PubMed]
- Tsubota T, Tajima R, Ode K, Kubota H, Fukuhara N, Kawabata T, Maki S, Maki H.
Double-stranded DNA binding, an unusual property of DNA polymerase epsilon , promotes epigenetic silencing in Saccharomyces cerevisiae.
J Biol Chem. 2006 Aug 16;
[PubMed]
- Ohta T, Kawabata T, Nishikawa K, Tani A, Kimbara K, Kawai F.
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.
Appl Environ Microbiol. 2006 Jun;72(6):4388-96.
[PubMed]
- Uehara K, Kawabata T, Go N.(2004).
Filtering remote homologues using predicted structural information.
Protein Eng Des Sel., 17, 565-570.
[PubMed]
- Kawabata,T. (2003) MATRAS: A Program for Protein 3D Structure Comparison.
Nucleic Acids Research, Vol. 31, pp. 3367-3369
[PubMed].
- Kawabata,T., Fukuchi,S., Homma, K., Ota,M., Araki,J., Ito,T., Ichiyoshi, N. and Nishikawa, K.(2002)
GTOP:a database of protein structures predicted from genome sequences Nucl. Acids Res., Vol.30, pp.294-298.
[PubMed]
- Kawabata,T. and Nishikawa,K. (2000) Protein structure comparison using the Markov transition model of evolution. Proteins, Vol 41, pp. 108-122.
[PubMed]
- Kawabata, T., Arisaka, F., and Nishikawa, K.(2000) Structural/functional assignment of unknown bacteriophage T4 proteins by iterative database searches. Genes, Vol.259, pp. 223-233.
[PubMed]
- Kawabata,T., Ota,M., and Nishikawa,K. (1999) The Protein Mutant Database.
Nucleic Acids Research, Vol 27, 355-357.
[PubMed]
[Go to PMD page]
- Ota M., Kawabata T., Kinjo,R.A., Nishikawa,K.(1999)
Cooperative Approach for the Protein Fold Recognition.
Proteins Suppl.3:126-132
[PubMed]
- Sagara,J., Shimizu,S., Kawabata,T., Nakamura,S.,
Ikeguchi,M., Shimizu,K.(1998)
The use of sequence comparison to detect identities in tRNA genes.
Nucleic Acids Research, Vol 26, 1974-1979
[PubMed]
- Kawabata, T. and Doi, J.(1997) Improvement of Protein Secondary Structure Prediction Using Binary Word Encoding. Proteins, Vol 27, pp. 36-46.
[PubMed]