1. Task force for considering the cancer education at Ministry of Education, Culture, Sports, Science
February 2023
19
A trial of web-based method to teach impact of genome variation
on protein structures at high school
and Technology. Report on the methods for cancer education at School (2016).
https://www.gankyouiku.mext.go.jp/download/cancer_education_report.pdf2.
2. Ministry of Education, Culture, Sports, Science and Technology. Results of Survey on Efforts to
Reform
School
Work
Styles
by
the
Board
of
Education
in
2020
(2020).
https://www.mext.go.jp/content/ 20201224-mxt_zaimu-000011455_1.pdf
3. Gojobori, 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. VaProS: A
Database-Integration Approach for Protein/Genome Information Retrieval. Journal of Structural
and Functional Genomics, 17, 69-81 (2016). https://doi.org/10.1007/s10969-016-9211-3
4. Howe, K.L., Achuthan, P., Allen, J., Allen, J., Alvarez-Jarreta, Amode, J.M.R., Armean, I.M., Azov,
A.G., Bennett, R., Bhai, J., Billis, K., Boddu, S., Charkhchi, M., Cummins, C., Fioretto, L.D.R.,
Davidson, C., Dodiya. K., Houdaigui, B.E., Fatima. R., Gall, A., Giron, C.G., Grego, T., GuijarroClarke, C., Haggerty, L., Hemrom, A., Hourlier, T., Izuogu, O.G., Juettemann, T., Kaikala, V., Kay,
M., Lavidas, I., Le, T., Lemos, D., Martinez, J.G., Marugán, J.C., McMahon, T.M.A.C., Mohanan,
S., Moore, B., Muffato, M, Oheh, D.N., Paraschas, D., Parker, A., Parton, A., Prosovetskaia, I.,
Sakthivel, M.P., Salam, A.I.A., Schmitt, B.M., Schuilenburg, H., Sheppard, D., Steed, E., Szpak,
M., Szuba, M., Taylor, K., Thormann, A., Threadgold, G., Walts, B., Winterbottom, A.,
Chakiachvili, M., Chaubal, A., Silva, N.D., Flint, B., Frankish, A., Hunt, S.E., IIsley. G.R.,
Langridge, N., Loveland, J.E., Martin, F.J., Mudge, J.M., Morales, J., Perry, E., Ruffier, M., Tate,
J., Thybert, D., Trevanion, S.J., Cunningham, F., Yates, A.D., Zerbino, D.R., Flicek, P. Ensembl
2021. Nucleic Acids Research, 49, 884–891 (2021). https://doi.org/10.1093/nar/gkaa942
5. Landrum, M. J., Chitipiralla, S., Brown, G. R., Chen, C., Gu, B., Hart, J., Hoffman, D., Jang, W.,
Kaur, K., Liu, C., Lyoshin, V., Maddipatla, Z., Maiti, R., Mitchell, J., O'Leary, N., Riley, G. R., Shi,
W., Zhou, G., Schneider, V., Maglott, D., Holmes, J.B., Kattman, B. L. ClinVar: improvements to
accessing
data.
Nucleic
Acids
Research,
48,
D835-D844
(2020).
https://doi.org/10.1093/nar/gkz972
6. Bekker, G-J., Yokochi, M., Suzuki, H., Ikegawa, Y., Iwata, T., Kudo, 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 3D macromolecular structural data. Protein Science, 31, 173186 (2022). https://doi.org/10.1002/pro.4211
7. Sali, A., Blundell, T.L. Comparative protein modelling by satisfaction of spatial restraints. Journal
of
Molecular
Biology,
234,
779-815
(1993).
https://doi.org/10.1006/jmbi.1993.1626,
https://modbase.compbio.ucsf.edu/modweb/
8. Chen, Y., Lu, H., Zhang, N., Chen, Y., Zhu, Z., Wang, S., Li, M. PremPS: Predicting the impact of
missense mutations on protein stability. PLoS Computational Biology, 16, e1008543 (2020).
https://doi.org/ 10.1371/journal.pcbi.1008543
20
Saki Katagiri, Mayu Shibata, Misae Kudo and Kei Yura
NSR. O., Vol. 73
9. Wiederstein, M., Sippl, M.J. (2007) ProSA-web: interactive web service for the recognition of errors
in three-dimensional structures of proteins. Nucleic Acids Research 35, W407-W410 (2007).
https://doi.org/10.1093/nar/gkm290, https://prosa.services.came.sbg.ac.at/prosa.php
10. Rose, A.S., Bradley, A.R., Valasatava, Y., Duarte, J.M., Prlic, A., Rose, P.W. NGL viewer: webbased molecular graphics for large complexes. Bioinformatics. 34, 3755-3758 (2018).
https://doi.org/10.1093/bioinformatics/bty419
11. Dominguez, R., Madasu, Y., Rao, J.N. Actin cytoskeleton. Mechanism of actin filament pointedend capping by tropomodulin. Science, 345, 463-467 (2014).
https://doi.org/10.1126/science.1256159
12. Brzovic, P.S., Hoyt, D.W., King, M.C., Klevit, R.E., Rajagopal, P. Structure of a BRCA1-BARD1
heterodimeric RING-RING complex. Nature. Structural & Molecular Biology, 8, 833-837 (2001).
https://doi.org/10.1038/nsb1001-833
13. Abraham, D.J., Ko, T.P., Musayev, F.N., Safo, M.K., Wu, S.H. Structure of tetragonal crystals of
human erythrocyte catalase. Acta Crystallography Section D, 57, 1-7 (2001).
https://doi.org/10.1107/s0907444900013767
14. Bauer, R., Boudko, S.P., Chetyrkin, S.V., Hudson, B.G., Ivanov, S., Smith, J., Voziyan, P.A.
Collagen IV345 dysfunction in glomerular basement membrane diseases. II. Crystal structure of
the 345 hexamer. Journal of Biological Chemistry, 296, 100591-100591 (2021).
https://doi.org/10.1016/j.jbc.2021.100591
15. Bowley, S.R., Lord, S.T. Fibrinogen variant BbetaD432A has normal polymerization but does not
bind knob "B". Blood, 113, 4425-4430 (2009). https://doi.org/10.1182/blood-2008-09-178178
16. Fermi, G., Fourme, R., Perutz, M.F., Shaanan, B. The crystal structure of human
deoxyhaemoglobin at 1.74 A resolution. Journal of Molecular Biology, 175, 159-174, (1984).
https://doi.org/ 10.1016/0022-2836(84)90472-8
17. Brange, J., Chance, K., Dodson, G.G., Finch, J., Scott, D.J., Whittingham, J.L., Wilson, A. Insulin
at pH 2: Structural analysis of the conditions promoting insulin fibre formation. Journal of
Molecular Biology, 318, 479-490, (2002). https://doi.org/10.1016/S0022-2836(02)00021-9
18. Bunick, C.G., Milstone, L.M. The X-Ray crystal structure of the keratin 1-keratin 10 helix 2B
heterodimer reveals molecular surface properties and biochemical insights into human skin disease.
Journal of Investigative Dermatology, 137, 142-150 (2017).
https://doi.org/10.1016/j.jid.2016.08.018
19. Adaixo, R., Dawson, R.J., Deupi, X., Flock, T., Maeda, S., Marino, J., Matile, H., Mohammed, I.,
Muehle, J., Pamula, F., Schertler, G., Stahlberg, H., Taylor, N.M., Tsai, C.J. Cryo-EM structure of
the rhodopsin-Gi- complex reveals binding of the rhodopsin C-terminal tail to the G subunit.
elife, 8, e46041 (2019). https://doi.org/10.7554/eLife.46041
20. Carrell, R.W., Chan, W.L., Ley, S.V., Loiseau, F., Milroy, L.G., Myers, R.M., Qi, X., Read, R.J.,
February 2023
A trial of web-based method to teach impact of genome variation
on protein structures at high school
Wei, Z., Yan, Y.,Zhou, A. Allosteric modulation of hormone release from thyroxine and
corticosteroid binding-globulins. Journal of Biological Chemistry, 286, 16163-16173 (2011).
https://doi.org/10.1074/jbc.M110.171082
21. Duong, H.T.T., Suzuki, H., Katagiri, S., Shibata, M., Arai, M., Yura, K. Computational study of
the impact of nucleotide variations on highly conserved proteins: In the case of actin. Biophysics
and Physicobiology, 19, 3190025 (2022). https://doi.org/10.2142/biophysico.bppb-v19.0025
22. Momozawa, Y., Sasai, R., Usui, Y., Shiraishi, K., Iwasaki, Y., Taniyama, Y. Parsons, M.T.,
Mizukami, K., Sekine, Y., Hirata, M., Kamatani, Y., Endo, M., Inai, C., Takata, S., Ito, H., Kohno,
T., Matsuda, K., Nakamura, S., Sugano, K., Yoshida, T., Nakagawa, H., Matsuo. K., Murakami, Y.,
Spurdle, A.B., Kubo, M. Expansion of Cancer Risk Profile for BRCA1 and BRCA2 Pathogenic
Variants. JAMA Oncology, 8, 871–878 (2022). https://10.1001/jamaoncol.2022.0476
Saki Katagiri
Address: Graduate School of Humanities and Sciences, Ochanomizu University, 2-1-1 Otsuka, Bunkyo,
Tokyo 112-8610, Japan
E-mail: g2170501@edu.cc.ocha.ac.jp
Mayu Shibata
Address: Graduate School of Humanities and Sciences, Ochanomizu University, 2-1-1 Otsuka, Bunkyo,
Tokyo 112-8610, Japan
E-mail: g2170503@edu.cc.ocha.ac.jp
Misae Kudo
Address: Graduate School of Humanities and Sciences, Ochanomizu University, 2-1-1 Otsuka, Bunkyo,
Tokyo 112-8610, Japan
E-mail: g2140547@edu.cc.ocha.ac.jp
Kei Yura
Address: Graduate School of Humanities and Sciences, Ochanomizu University, 2-1-1 Otsuka, Bunkyo,
Tokyo 112-8610, Japan. Center for Interdisciplinary AI and Data Science, Ochanomizu
University, 2-1-1 Otsuka, Bunkyo, Tokyo 112-8610, Japan.
E-mail: yura.kei@ocha.ac.jp
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