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Search</a><a title="PDBj Omni Search Help" href="/help/omni-search">Search help</a></div></div></header><div><main id=""><div class="sNP" typeof="Article"><h1 property="name headline">List of Publications</h1><div><div class="OGhover opacityTransition2 _langList_" style="margin-left: 3em;"><span>This page is also available in: </span><a title="日本語" href="/info/publications?lang=ja" style="margin-right: 0.75em;">日本語</a><hr class="leftHR"></div><div property="articleBody" class="BLOG_BOX"> <style type="text/css"></style> <ul class="citation"> <li> <ul class="citationitem"> <li><span class="cite_maintitle">Fifty years of Protein Data Bank in the Journal of Biochemistry</span></li> <li class="cite_author">Genji Kurisu</li> <li class="cite_journal">The Journal of Biochemistry</li> <li class="cite_volume">171(1)</li> <li class="cite_page">3-11</li> <li class="cite_year">2022</li> <li class="cite_doi"><a href="https://doi.org/10.1093/jb/mvab133" rel="nofollow noopener" target="_blank">10.1093/jb/mvab133</a></li> </ul> </li> <li> <ul class="citationitem"> <li><span class="cite_maintitle">Forty years of the structure of plant-type ferredoxin</span></li> <li class="cite_author">Genji Kurisu, Tomitake Tsukihara</li> <li class="cite_journal">The Journal of Biochemistry</li> <li class="cite_volume">171(1)</li> <li class="cite_page">19-21</li> <li class="cite_year">2022</li> <li class="cite_doi"><a href="https://doi.org/10.1093/jb/mvab113" rel="nofollow noopener" target="_blank">10.1093/jb/mvab113</a></li> </ul> </li> <li> <ul class="citationitem"> <li><span class="cite_maintitle">Protein Data Bank Japan: Celebrating our 20th anniversary during a global pandemic as the Asian hub of three dimensional macromolecular structural data</span></li> <li class="cite_author">Gert-Jan Bekker, Masashi Yokochi, Hirofumi Suzuki, Yasuyo Ikegawa, Takeshi Iwata, Takahiro Kudou, Kei Yura, Toshimichi Fujiwara, Takeshi Kawabata, Genji Kurisu</li> <li class="cite_journal">Protein Science</li> <li class="cite_volume">31(1)</li> <li class="cite_page">173-186</li> <li class="cite_year">2022</li> <li class="cite_doi"><a href="https://doi.org/10.1002/pro.4211" rel="nofollow noopener" target="_blank">10.1002/pro.4211</a></li> </ul> </li> <li> <ul class="citationitem"> <li><span class="cite_maintitle">Enhanced validation of small-molecule ligands and carbohydrates in the protein databank</span></li> <li class="cite_author">Zukang Feng, John D.Westbrook, Raul Sala, Oliver S.Smart, Gérard Bricogne, Masaaki Matsubara, Issaku Yamada, Shinichiro Tsuchiya, Kiyoko F.Aoki-Kinoshita, Jeffrey C.Hoch, Genji Kurisu, Sameer Velankar, Stephen K.Burley, Jasmine Y.Young</li> <li class="cite_journal">Structure</li> <li class="cite_volume">29</li> <li class="cite_page">1-8</li> <li class="cite_year">2021</li> <li class="cite_doi"><a href="http://doi.org/10.1016/j.str.2021.02.004" rel="nofollow noopener" target="_blank">10.1016/j.str.2021.02.004</a></li> </ul> </li> <li> <ul class="citationitem"> <li><span class="cite_maintitle">BioMagResBank (BMRB) as a Resource for Structural Biology</span></li> <li class="cite_author">Pedro R. Romero, Naohiro Kobayashi, Jonathan R. Wedell, Kumaran Baskaran, Takeshi Iwata, Masashi Yokochi, Dimitri Maziuk, Hongyang Yao, Toshimichi Fujiwara, Genji Kurusu, Eldon L. Ulrich, Jeffrey C. Hoch, John L. Markley</li> <li class="cite_journal">Structural Bioinformatics. Methods in Molecular Biology</li> <li class="cite_volume">2112</li> <li class="cite_page">187-218</li> <li class="cite_year">2020</li> </ul> </li> <li id="ref1_2019"> <b>Protein Data Bank: the single global archive for 3D macromolecular structure data</b><br> wwPDB consortium<br> <em>Nucleic Acids Research</em><b> 47</b>(D1): D520-D528 (2019) <a href="http://www.ncbi.nlm.nih.gov/pubmed/30357364" rel="nofollow noopener" target="_blank">[PubMed]</a> <a href="http://doi.org/10.1093/nar/gky949" rel="nofollow noopener" target="_blank">[doi:10.1093/nar/gky949]</a> </li> <li> <b>New tools and functions in Data-out activities at Protein Data Bank Japan (PDBj)</b><br> Kinjo, A.R., Bekker, G.-J., 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. and Nakamura, H.<br> <em>Protein Science</em><b> 27</b> (1): 95-102 (2018) <a href="http://www.ncbi.nlm.nih.gov/pubmed/28815765" rel="nofollow noopener" target="_blank">[PubMed]</a> <a href="http://dx.doi.org/10.1002/pro.3273" rel="nofollow noopener" target="_blank">[doi:10.1002/pro.3273]</a> </li> <li> <b>Protein Data Bank Japan (PDBj): Updated user interfaces, Resource Description Framework, analysis tools for large structures</b><br> Kinjo, A.R., Bekker, G.-J., Suzuki, H., Tsuchiya, Y., Kawabata, T., Ikegawa, Y., Nakamura, H.<br> <em>Nucleic Acids Research</em><b> 45</b>(D1): D282-D288 (2017) <a href="http://dx.doi.org/10.1093/nar/gkw962" rel="nofollow noopener" target="_blank">[doi:10.1093/nar/gkw962]</a> </li> <li> <b>Molmil: a molecular viewer for the PDB and beyond</b><br> Bekker, G.-J., Nakamura, H., Kinjo, A.R.<br> <em>Journal of Cheminformatics</em><b> 8</b>:42 (2016) <a href="http://dx.doi.org/10.1186/s13321-016-0155-1" rel="nofollow noopener" target="_blank">[doi:10.1186/s13321-016-0155-1]</a> </li> <li> <b>Omokage search: shape similarity search service for biomolecular structures in both the PDB and EMDB</b><br> Suzuki, H., Kawabata, T., Nakamura, H.<br> <em>Bioinformatics</em><b> 32</b> (4): 619-620 (2016) <a href="http://www.ncbi.nlm.nih.gov/pubmed/26508754" rel="nofollow noopener" target="_blank">[PubMed]</a> <a href="http://dx.doi.org/10.1093/bioinformatics/btv614" rel="nofollow noopener" target="_blank">[doi:10.1093/bioinformatics/btv614]</a> </li> <li> <b>A novel loss-of-function mutation of GATA3 (p.R299Q) in a Japanese family with Hypoparathyroidism, Deafness, and Renal Dysplasia (HDR) syndrome</b><br> Okawa, T., Yoshida, M., Usui, T., Kudou, T., Iwasaki, Y., Fukuoka, K., Takahashi, N., Uehara, Y., Oiso, Y.<br> <em>BMC Endocrine Disorders</em><b> 15</b>: 66 (2015) <a href="http://dx.doi.org/10.1186/s12902-015-0065-7" rel="nofollow noopener" target="_blank">[doi:10.1186/s12902-015-0065-7]</a> </li> <li> <b>The Protein Data Bank archive as an open data resource</b><br> Berman, H.M., Kleywegt, G.J., Nakamura, H., Markley, J.L.<br> <em>Journal of Computer-Aided Molecular Design</em><b> 28</b> (10): 1009-1014 (2014) <a href="http://dx.doi.org/10.1007/s10822-014-9770-y" rel="nofollow noopener" target="_blank">[doi:10.1007/s10822-014-9770-y]</a> </li> <li> <b>How Community Has Shaped the Protein Data Bank</b><br> Berman, H.M., Kleywegt, G.J., Nakamura, H., Markley, J.L.<br> <em>Structure</em><b> 21</b> (9): 1485-1491 (2013) <a href="http://dx.doi.org/10.1016/j.str.2013.07.010" rel="nofollow noopener" target="_blank">[doi:10.1016/j.str.2013.07.010]</a> </li> <li> <b>Exhaustive comparison and classification of ligand-binding surfaces in proteins. </b><br> Murakami, Y., Kinoshita, K., Kinjo, A.R., Nakamura, H.<br> <em>Protein Science</em><b> 22</b> (10): 1379-1391 (2013) <a href="http://www.ncbi.nlm.nih.gov/pubmed/23934772" rel="nofollow noopener" target="_blank">[PubMed]</a> <a href="http://dx.doi.org/10.1002/pro.2329" rel="nofollow noopener" target="_blank">[doi:10.1002/pro.2329]</a> </li> <li> <b>Normal mode analysis based on an elastic network model for biomolecules in the Protein Data Bank, which uses dihedral angles as independent variables.</b><br> Wako, H., Endo, S.<br> <em>Comp.Biol.Chem.</em><b> 44</b> 22-30 (2013) <a href="http://www.ncbi.nlm.nih.gov/pubmed/23537565" rel="nofollow noopener" target="_blank">[PubMed]</a> <a href="http://dx.doi.org/10.1016/j.compbiolchem.2013.02.006" rel="nofollow noopener" target="_blank">[doi:10.1016/j.compbiolchem.2013.02.006]</a> </li> <li> <b>Functional structural motifs for protein-ligand, protein-protein and protein-nucleic acid interactions and their connection to supersecondary structures. </b><br> Kinjo, A.R., Nakamura, H.<br> <em>Methods in Molecular Biology</em><b> 932:</b> 295-315 (2013) <a href="http://www.ncbi.nlm.nih.gov/pubmed/22987360" rel="nofollow noopener" target="_blank">[PubMed]</a> <a href="http://dx.doi.org/10.1007/978-1-62703-065-6_18" rel="nofollow noopener" target="_blank">[doi:10.1007/978-1-62703-065-6_18]</a> </li> <li> <b>The Protein Data Bank at 40: Reflecting on the Past to Prepare for the Future</b><br> Berman, H.M., Kleywegt, G.J., Nakamura, H., Markley, J.L.<br> <em>Structure</em><b> 20</b> (3): 391-396 (2012) <a href="http://www.ncbi.nlm.nih.gov/pubmed/22404998" rel="nofollow noopener" target="_blank">[PubMed]</a> <a href="http://dx.doi.org/10.1016/j.str.2012.01.010" rel="nofollow noopener" target="_blank">[doi:10.1016/j.str.2012.01.010]</a> </li> <li> <b>The future of the protein data bank.</b><br> Berman, H.M., Kleywegt, G.J., Nakamura, H., Markley, J.L.<br> <em>Biopolymers</em><b> 99</b> (2): (2012) <a href="http://www.ncbi.nlm.nih.gov/pubmed/23023942" rel="nofollow noopener" target="_blank">[PubMed]</a> <a href="http://dx.doi.org/10.1002/bip.22132" rel="nofollow noopener" target="_blank">[doi:10.1002/bip.22132]</a> </li> <li> <b>GIRAF: a method for fast search and flexible alignment of ligand binding interfaces in proteins at atomic resolution.</b><br> Kinjo, A.R., Nakamura, H.<br> <em>BIOPHYSICS</em><b> 8:</b> 79-94 (2012) <a href="http://dx.doi.org/10.2142/biophysics.8.79" rel="nofollow noopener" target="_blank">[doi:10.2142/biophysics.8.79]</a> </li> <li> <b>Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format.</b><br> Kinjo, A.R., Suzuki, H., Yamashita, R., Ikegawa, Y., Kudou, T., Igarashi, R., Kengaku, Y., Cho, H., Standley, D.M., Nakagawa, A., Nakamura, H. <br> <em>Nucleic Acids Research</em><b> 40</b>(D1): D453-D460 (2012) <a href="http://www.ncbi.nlm.nih.gov/pubmed/21976737" rel="nofollow noopener" target="_blank">[PubMed]</a> <a href="http://dx.doi.org/10.1093/nar/gkr811" rel="nofollow noopener" target="_blank">[doi:10.1093/nar/gkr811]</a> </li> <li> <b>A comparative study of conservation and variation scores</b><br> Johansson, F., Toh, H.<br> <em>BMC Bioinformatics</em><b> 11</b>: (2010) <a href="http://www.ncbi.nlm.nih.gov/pubmed/20663120" rel="nofollow noopener" target="_blank">[PubMed]</a> <a href="http://dx.doi.org/10.1186/1471-2105-11-388" rel="nofollow noopener" target="_blank">[doi:10.1186/1471-2105-11-388]</a> </li> <li> <b>Relative von neumann entropy for evaluating amino Acid conservation</b><br> Johansson, F., Toh, H.<br> <em>J Bioinform Comput Biol</em><b> 8</b>(5): 809-823 (2010) <a href="http://www.ncbi.nlm.nih.gov/pubmed/20981889" rel="nofollow noopener" target="_blank">[PubMed]</a> <a href="http://dx.doi.org/10.1142/S021972001000494X" rel="nofollow noopener" target="_blank">[doi:10.1142/S021972001000494X]</a> </li> <li> <b>PDBj Mine: Design and implementation of relational database interface for Protein Data Bank Japan</b><br> Kinjo, A.R., Yamashita, R., Nakamura, H.<br> <em>Database</em><b> 2010</b>: baq021 (2010) <a href="http://www.ncbi.nlm.nih.gov/pubmed/20798081" rel="nofollow noopener" target="_blank">[PubMed]</a> <a href="http://dx.doi.org/10.1093/database/BAQ021" rel="nofollow noopener" target="_blank">[doi:10.1093/database/BAQ021]</a> </li> <li> <b>Geometric similarities of protein-protein interfaces at atomic resolution are only observed within homologous families: An exhaustive structural classification study</b><br> Kinjo, A.R., Nakamura, H.<br> <em>Journal of Molecular Biology</em><b> 399</b>: 526-540 (2010) <a href="http://www.ncbi.nlm.nih.gov/pubmed/20417638" rel="nofollow noopener" target="_blank">[PubMed]</a> <a href="http://dx.doi.org/10.1016/j.jmb.2010.04.028" rel="nofollow noopener" target="_blank">[doi:10.1016/j.jmb.2010.04.028]</a> </li> <li> <b>SeSAW: balancing sequence and structural information in protein functional mapping.</b><br> Standley, D.M., Yamashita, R., Kinjo, A.R., Toh, H., Nakamura, H.<br> <em>Bioinformatics</em><b> 26</b>: 1258-1259(2010) <a href="http://www.ncbi.nlm.nih.gov/pubmed/20299324" rel="nofollow noopener" target="_blank">[PubMed]</a> <a href="http://dx.doi.org/10.1093/bioinformatics/btq116" rel="nofollow noopener" target="_blank">[doi:10.1093/bioinformatics/btq116]</a> </li> <li> <b>Outcome of a Workshop on Applications of Protein Models in Biomedical Research </b><br> Schwede, T., Sali, A., Honig, B., Levitt, M., Berman, H.M., Jones, D., Brenner, S.E., Burley, S.K., Das, R., Dokholyan, N.V., Dunbrack Jr., R.L., Fidelis, K., Fiser, A., Godzik, A., Huang, Y.J., Humblet, C., Jacobson, M.P., Joachimiak, A., Krystek Jr., S.R., Kortemme, T., Kryshtafovych, A., Montelione, G.T., Moult, J., Murray, D., Sanchez, R., Sosnick, T.R., Standley, D.M., Stouch, T., Vajda, S., Vasquez, M., Westbrook, J.D., Wilson, I.A.<br> <em>Structure</em><b> 17</b> (2): 151-159 (2009) <a href="http://www.ncbi.nlm.nih.gov/pubmed/19217386" rel="nofollow noopener" target="_blank">[PubMed]</a> <a href="http://dx.doi.org/10.1016/j.str.2008.12.014" rel="nofollow noopener" target="_blank">[doi:10.1016/j.str.2008.12.014]</a> </li> <li> <b>Data Deposition and Annotation at the Worldwide Protein Data Bank </b><br> Dutta, S., Burkhardt, K., Young, J., Swaminathan, G.J., Matsuura, T., Henrick, K., Nakamura, H., Berman, H.M.<br> <em>Mol. Biotechnol.</em><b> 42</b> (1): 1-13 (2009) <a href="http://www.ncbi.nlm.nih.gov/pubmed/19082769" rel="nofollow noopener" target="_blank">[PubMed]</a> <a href="http://dx.doi.org/10.1007/s12033-008-9127-7" rel="nofollow noopener" target="_blank">[doi:10.1007/s12033-008-9127-7]</a> </li> <li> <b>Comprehensive structural classification of ligand-binding motifs in proteins</b><br> Kinjo, A.R., Nakamura, H.<br> <em>Structure</em><b> 17</b> (2): 234-246 (2009) <a href="http://www.ncbi.nlm.nih.gov/pubmed/19217394" rel="nofollow noopener" target="_blank">[PubMed]</a> <a href="http://dx.doi.org/10.1016/j.str.2008.11.009" rel="nofollow noopener" target="_blank">[doi:10.1016/j.str.2008.11.009]</a> </li> <li> <b>Structure-based functional annotation of protein sequences guided by comparative models</b><br> Standley, D.M., Kinjo, A.R., Lis, M., van der Giezen, M., Nakamura, H. <br> <em>Proceedings of the Second International Symposium on Optimization and Systems Biology</em> (ed. Luonan Chen) Lijiang China.<b></b> 395-403 (2008) <a href="http://www.aporc.org/LNOR/9/OSB2008F50.pdf" rel="nofollow noopener" target="_blank">[pdf (at APORC website)]</a> </li> <li> <b>BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): new policies affecting biomolecular NMR depositions</b><br> Markley, J.L., Ulrich, E.L., Berman, H.M., Henrick, K., Nakamura, H., Akutsu, H.<br> <em>J. Biomol. NMR</em><b> 40</b> (3): 153-155 (2008) <a href="http://www.ncbi.nlm.nih.gov/pubmed/18288446" rel="nofollow noopener" target="_blank">[PubMed]</a> <a href="http://dx.doi.org/10.1007/s10858-008-9221-y" rel="nofollow noopener" target="_blank">[doi:10.1007/s10858-008-9221-y]</a> </li> <li> <b>Remediation of the protein data bank archive</b><br> Henrick, K., Feng, Z., Bluhm, W.F., Dimitropoulos, D., Doreleijers, J.F., Dutta, S., Flippen-Anderson, J.L., Ionides, J., Kamada, C., Krissinel, E., Lawson, C.L., Markley, J.L., Nakamura, H., Newman, R., Shimizu, Y., Swaminathan, J., Velankar, S., Ory, J., E. Ulrich, E.L., Vranken, W., Westbrook, J.D., Yamashita, R., Yang, H., Young, J., Yousufuddin, M., Berman, H.M.<br> <em>Nucleic Acids Res.</em><b> 36</b> (Database issue): D426-D433 (2008) <a href="http://www.ncbi.nlm.nih.gov/pubmed/18073189" rel="nofollow noopener" target="_blank">[PubMed]</a> <a href="http://dx.doi.org/10.1093/nar/gkm937" rel="nofollow noopener" target="_blank">[doi:10.1093/nar/gkm937]</a> </li> <li> <b>BioMagResBank</b><br> Ulrich, E.L., Akutsu, H., Doreleijers, J.F., Harano, Y., Ioannidis, Y.E., Lin, J., Livny, M., Mading, S., Maziuk, D., Miller, Z., Nakatani, E., Schulte, C.F., Tolmie, D.E., Kent Wenger, R., Yao, H., Markley, J.L.<br> <em>Nucleic Acids Res.</em><b> 36</b> (Database issue): D402-408 (2008) <a href="http://dx.doi.org/10.1093/nar/gkm957" rel="nofollow noopener" target="_blank">[doi:10.1093/nar/gkm957]</a> </li> <b>Protein multiple sequence alignment</b><br> Do, C.B., Katoh, K.<br> <em>Methods in Molecular Biology</em><b> 484:</b> 379-413 (2008) <a href="http://www.ncbi.nlm.nih.gov/pubmed/18592193" rel="nofollow noopener" target="_blank">[PubMed]</a> <a href="http://dx.doi.org/10.1007/978-1-59745-398-1_25" rel="nofollow noopener" target="_blank">[doi:10.1007/978-1-59745-398-1_25]</a> <li> <b>Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework</b><br> Katoh, K., Toh, H.<br> <em>BMC Bioinformatics</em><b> 9:</b> 212-224 (2008) <a href="http://www.ncbi.nlm.nih.gov/pubmed/18439255" rel="nofollow noopener" target="_blank">[PubMed]</a> <a href="http://dx.doi.org/10.1186/1471-2105-9-212" rel="nofollow noopener" target="_blank">[doi:10.1186/1471-2105-9-212]</a> </li> <li> <b>Recent developments in the MAFFT multiple sequence alignment program</b><br> Katoh, K., Toh, H.<br> <em>Brief. 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