Publications

Yamamori, Y. & Tomii, K. Application of Homology Modeling by Enhanced Profile-Profile Alignment and Flexible-Fitting Simulation to Cryo-EM Based Structure Determination Int. J. Mol. Sci. , 23(4), 1977 (2022). [PubMed] doi: 10.3390/ijms23041977.

Kimura, K., Kawai, F., Kubota-Kawai, H. Watanabe, Y., Tomii, K., Kojima, R., Hirata, K., Yamamori, Y., Endo, T., & Tamura, Y. Crystal structure of Tam41 cytidine diphosphate diacylglycerol synthase from a Firmicutes bacterium J. Biochem., mvab154 (2021). [PubMed] doi: 10.1093/jb/mvab154.

Ikeda, K., Doi, T., Ikeda, M., & Tomii, K. PreBINDS: An Interactive Web Tool to Create Appropriate Datasets for Predicting Compound-Protein Interactions Front. Mol. Biosci., 8, 758480 (2021). [PubMed] doi: 10.3389/fmolb.2021.758480.

Tanaka, H., Kondo, K., Fujita, K., Homma, H., Tagawa, K., Jin, X., Jin, M., Yoshioka, Y., Takayama, S., Masuda, H., Tokuyama, R., Nakazaki, Y., Saito, T., Saido, T., Murayama, S., Ikura, T., Ito, N., Yamamori, Y., Tomii, K., Bianchi, M.E., & Okazawa, H. HMGB1 signaling phosphorylates Ku70 and impairs DNA damage repair in Alzheimer's disease pathology Communications biology, 4(1), 1175 (2021). [PubMed] doi: 10.1038/s42003-021-02671-4.

Kryshtafovych, A., Moult, J., Billings, W.M., Della Corte, D., Fidelis, K., Kwon, S., Olechnovič, K., Seok, C., Venclovas, Č., Won, J., & CASP-COVID participants. Modeling SARS-CoV-2 proteins in the CASP-commons experiment. Proteins (2021). [PubMed] doi: 10.1002/prot.26231.

Grapotte, M., Saraswat, M., Bessière, C., Menichelli, C., Ramilowski, J.A., Severin, J., Hayashizaki, Y., Itoh, M., Tagami, M., Murata, M., Kojima-Ishiyama, M., Noma, S., Noguchi S., Kasukawa T., Hasegawa A., ,,, FANTOM consortium, Chatelain, C., Carninci, P., de Hoon, M.J.L., Wasserman, W.W., Bréhélin, L. & Lecellier, C.-H. Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network. Nat. Communm., 12(1), 3297 (2021). [PubMed] doi: 10.1038/s41467-021-23143-7.

Yamamori, Y. & Tomii, K. An ensemble reweighting method for combining the information of experiments and simulations. Chemical Physics Letters, 779, 138821 (2021). [ScienceDirect] doi: 10.1016/j.cplett.2021.138821.

Takeda, H., Tsutsumi, A., Nishizawa, T., Lindau, C., Busto, J.V., Wenz, L.S., Ellenrieder, L., Imai, K., Straub, S.P., Mossmann, W., Qiu. J., Yamamori, Y., Tomii, K., Suzuki, J., Murata, T., Ogasawara, S., Nureki, O., Becker, T., Pfanner, N., Wiedemann, N., Kikkawa, M. & Endo, T. Mitochondrial sorting and assembly machinery operates by β-barrel switching. Nature, 590(7844), 163-169 (2021). [PubMed] doi: 10.1038/s41586-020-03113-7.

Saito-Nakano, Y., Wahyuni, R., Nakada-Tsukui, K., Tomii, K. & Nozaki T. Rab7D small GTPase is involved in phago-, trogocytosis and cytoskeletal reorganization in the enteric protozoan Entamoeba histolytica. Cell Microbiol., 23(1), e13267 (2020). [PubMed] doi: 10.1111/cmi.13267.

Santos, H.J., Chiba, Y., Makiuchi, T., Arakawa, S., Murakami, Y., Tomii, K., Imai, K. & Nozaki T. Import of Entamoeba histolytica Mitosomal ATP Sulfurylase Relies on Internal Targeting Sequences. Microorganisms, 8(8), 1229 (2020). [PubMed] doi: 10.3390/microorganisms8081229.

Umeno, A., Sakashita, M., Sugino, S., Murotomi, K., Okuzawa, T., Morita, N., Tomii, K. Tsuchiya, Y., Yamasaki, K., Horie, M., Takahara, K. & Yoshida, Y. Comprehensive analysis of PPARγ agonist activities of stereo-, regio-, and enantio-isomers of hydroxyoctadecadienoic acids. Bioscience reports, 40(4), BSR20193767 (2020). [PubMed] doi: 10.1042/BSR20193767.

Tsuchiya, Y. & Tomii, K. Neural networks for protein structure and function prediction and dynamic analysis. Biophysical Reviews, 12(2), 569-573 (2020). [PubMed] doi: 10.1007/s12551-020-00685-6.

Fukuda, H. & Tomii, K. DeepECA: an end-to-end learning framework for protein contact prediction from a multiple sequence alignment. BMC Bioinformatics, 21(1), 10 (2020). [PubMed] doi: 10.1186/s12859-019-3190-x.

Furuichi, T., Tsukamoto, M., Saito, M., Sato Y., Oiji, N., Yagami, K., Fukumura, R., Gondo, Y., Guo L., Ikegawa S., Yamamori, Y. & Tomii, K. Crim1 C140S Mutant Mice Reveal the Importance of Cysteine 140 in the Internal Region 1 of CRIM1 for Its Physiological Functions. Mamm. Genome, 30(11-12), 329-338 (2019). [PubMed] doi: 10.1007/s00335-019-09822-3.

Tomii, K., Santos, H.J. & Nozaki, T. Genome-Wide Analysis of Known and Potential Tetraspanins in Entamoeba histolytica. Genes, 10(11), 885 (2019). [PubMed] doi: 10.3390/genes10110885.

Santos, H.J., Imai, K., Makiuchi, T., Tomii, K., Horton, P., Nozawa, A., Okada, K., Tozawa, Y., Nozaki, T. Novel lineage-specific transmembrane beta-barrel proteins in the endoplasmic reticulum of Entamoeba histolytica. FEBS J., 286(17), 3416-3432 (2019). [PubMed] doi: 10.1111/febs.14870.

Fukasawa, Y. & Tomii K. Accurate Classification of Biological and non-Biological Interfaces in Protein Crystal Structures using Subtle Covariation Signals. Sci. Rep. 9(1), 12603 (2019). [PubMed] doi: 10.1038/s41598-019-48913-8.

Tsubaki, M., Tomii K. & Sese, J. Compound-protein Interaction Prediction with End-to-end Learning of Neural Networks for Graphs and Sequences. Bioinformatics. 35(2), 309-318 (2019). [PubMed] doi: 10.1093/bioinformatics/bty535.

Nakamura, T., Yamada, K.D., Tomii K. & Katoh K. Parallelization of MAFFT for large-scale multiple sequence alignments. Bioinformatics. 34(14), 2490-2492 (2018). [PubMed] doi: 10.1093/bioinformatics/bty121.

Nakada-Tsukui, K., Sekizuka, T., Sato-Ebine, E., Escueta-de Cadiz, A., Ji, D.D., Tomii K., Kuroda, M. & Nozaki, T. AIG1 affects in vitro and in vivo virulence in clinical isolates of Entamoeba histolytica. PLoS Pathog. 14(3), e1006882 (2018). [PubMed] doi: 10.1371/journal.ppat.1006882.

Nemoto, K., Kagawa, M., Nozawa, A., Hasegawa, Y., Hayashi, M., Imai, K., Tomii, K. & Sawasaki, T. Identification of new abscisic acid receptor agonists using a wheat cell-free based drug screening system. Sci. Rep. 8(1), 4268 (2018). [PubMed] doi: 10.1038/s41598-018-22538-9.

Nakamura, T., Oda, T., Fukasawa, Y. & Tomii, K. Template-based quaternary structure prediction of proteins using enhanced profile-profile alignments. Proteins. 86(Suppl. 1), 274-282 (2018). [PubMed] doi: 10.1002/prot.25432.

Nemoto, K., Ramadan, A., Arimura, G.I., Imai, K., Tomii, K., Shinozaki, K. & Sawasaki, T. Tyrosine phosphorylation of the GARU E3 ubiquitin ligase promotes gibberellin signalling by preventing GID1 degradation. Nat. Communm., 8(1), 1004 (2017). [PubMed] doi: 10.1038/s41467-017-01005-5.

Shiga, Y., Murata, D., Sugimoto, A., Oshima, Y., Tada, M., Ishii-Watabe, A., Imai, K., Tomii, K., Takeuchi, T., Kagaya, S. & Sato A. Hinge-Deficient IgG1 Fc Fusion: Application to Human Lactoferrin. Mol. Pharm., 14(9), 3025-3035 (2017). [PubMed] doi: 10.1021/acs.molpharmaceut.7b00221.

Yamada, K.D., Kunishima, N., Matsuura, Y., Nakai, K., Naitow, H., Fukasawa, Y. & Tomii, K. Designing better diffracting crystals of biotin carboxyl carrier protein from Pyrococcus horikoshii by a mutation based on the crystal-packing propensity of amino acids. Acta Crystallogr. D Struct. Biol., 73(Pt 9), 757-766 (2017). [PubMed] doi: 10.1107/S2059798317010932.

Oda, T., Lim, K. & Tomii, K. Simple adjustment of the sequence weight algorithm remarkably enhances PSI-BLAST performance. BMC Bioinformatics, 18(1), 288 (2017). [PubMed] doi: 10.1186/s12859-017-1686-9.

Fukasawa, Y., Oda, T., Tomii, K. & Imai, K. Origin and Evolutionary Alteration of the Mitochondrial Import System in Eukaryotic Lineages. Mol. Biol. Evol., 34(7), 1574-1586 (2017). [PubMed] doi: 10.1093/molbev/msx096.

Lim, K., Yamada, K.D., Frith, M.C. & Tomii, K. Protein sequence-similarity search acceleration using a heuristic algorithm with a sensitive matrix. J. Struct. Funct. Genomics, 17(4), 147-154 (2016). [PubMed] doi: 10.1007/s10969-016-9210-4.

Yamada, K.D., Tomii, K. & Katoh, K. Application of the MAFFT sequence alignment program to large data-reexamination of the usefulness of chained guide trees. Bioinformatics, 32(21), 3246-3251 (2016). [PubMed] doi: 10.1093/bioinformatics/btw412.

Imamura, T., Fujita, K., Tagawa, K., Ikura, T., Chen, X., Homma, H., Tamura, T., Mao, Y., Taniguchi, J.B., Motoki, K., Nakabayashi, M., Ito, N., Yamada, K., Tomii, K., Okano, H., Kaye, J., Finkbeiner, S. & Okazawa, H. Identification of hepta-histidine as a candidate drug for Huntington's disease by in silico-in vitro- in vivo-integrated screens of chemical libraries. Sci. Rep., 6, 33861 (2016). [PubMed] doi: 10.1038/srep33861.

Lensink, M.F., Velankar, S., Kryshtafovych, A., Huang, S.Y., Schneidman-Duhovny, D., Sali, A., Segura, J., Fernandez-Fuentes, N., Viswanath, S., Elber, R., Grudinin, S., Popov, P., Neveu, E., Lee, H., Baek, M., Park, S., Heo, L., Lee, G.R., Seok, C., Qin,S., Zhou, HX., Ritchie, D.W., Maigret, B., Devignes, M.D., Ghoorah, A., Torchala, M., Chaleil, R.A., Bates, P.A., Ben-Zeev, E., Eisenstein, M., Negi, S.S., Weng, Z., Vreven, T., Pierce, B.G., Borrman, T.M., Yu, J., Ochsenbein, F., Guerois, R., Vangone, A., Rodrigues, J.P., van Zundert, G., Nellen, M., Xue, L., Karaca, E., Melquiond, A.S., Visscher, K., Kastritis, P.L., Bonvin, A.M., Xu, X., Qiu, L., Yan, C., Li, J., Ma, Z., Cheng, J., Zou,X., Shen, Y., Peterson, L.X., Kim, H.R., Roy, A., Han, X., Esquivel-Rodriguez, J., Kihara, D., Yu, X., Bruce, N.J., Fuller, J.C., Wade, R.C., Anishchenko, I., Kundrotas, P.J., Vakser, I.A., Imai, K., Yamada, K., Oda, T., Nakamura, T., Tomii, K., Pallara, C., Romero-Durana, M., Jimenez-Garcia, B., Moal, I.H., Fernandez-Recio, J., Joung, J.Y., Kim, J.Y., Joo, K., Lee, J., Kozakov, D., Vajda, S., Mottarella, S., Hall, D.R., Beglov, D., Mamonov, A., Xia, B., Bohnuud, T., Del Carpio, C.A., Ichiishi, E., Marze, N., Kuroda, D., Roy Burman, S.S., Gray, J.J., Chermak, E., Cavallo, L., Oliva, R., Tovchigrechko, A. & Wodak, S.J. Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment. Proteins, 84(Suppl. 1), 323-348 (2016). [PubMed] doi: 10.1002/prot.25007.

Moya, A., Sakamaki, K., Mason, B.M., Huisman, L., Foret, S., Weiss, Y., Bull, T.E., Tomii, K., Imai, K., Hayward, D.C., Ball, E.E. & Miller, D.J. Functional conservation of the apoptotic machinery from coral to man: the diverse and complex Bcl-2 and caspase repertoires of Acropora millepora. BMC Genomics 17, 62 (2016). [PubMed] doi: 10.1186/s12864-015-2355-x.

Nakamura, T. & Tomii, K. Effects of the difference in similarity measures on the comparison of ligand-binding pockets using a reduced vector representation of pockets. Biophys. Physicobiol. 13, 139-147 (2016). [PubMed] doi: 10.2142/biophysico.13.0_139.

Nakamura, T. & Tomii, K. Protein ligand-binding site comparison by a reduced vector representation derived from multidimensional scaling of generalized description of binding sites. Methods 93, 35-40 (2016). [PubMed] doi: 10.1016/j.ymeth.2015.08.007.

Nagano, N., Umemura, M., Izumikawa, M., Kawano, J., Ishii, T., Kikuchi, M., Tomii, K., Kumagai, T., Yoshimi, A., Machida, M., Abe, K., Shin-Ya, K. & Asai, K.1 Class of cyclic ribosomal peptide synthetic genes in filamentous fungi. Fungal Genet. Biol. 86, 58-70 (2016). [PubMed] doi: 10.1016/j.fgb.2015.12.010.

Shiota, T., Imai, K., Qiu, J., Hewitt, V.L., Tan, K., Shen, H.H., Sakiyama, N., Fukasawa, Y., Hayat, S., Kamiya, M., Elofsson, A., Tomii, K., Horton, P., Wiedemann, N., Pfanner, N., Lithgow, T. & Endo, T. Molecular architecture of the active mitochondrial protein gate. Science 349(6255), 1544-1548 (2015). [PubMed] doi: 10.1126/science.aac6428.

Sakamaki, K., Iwabe, N., Iwata, H., Imai, K., Takagi, C., Chiba, K., Shukunami, C., Tomii, K. & Ueno, N. Conservation of structure and function in vertebrate c-FLIP proteins despite rapid evolutionary change. Biochem. Biophys. Reports 3, 175-189 (2015). [ScienceDirect] doi: 10.1016/j.bbrep.2015.08.005.

Kakisaka, M., Sasaki, Y., Yamada, K., Kondoh, Y., Hikono, H., Osada, H., Tomii, K. Saito, T. & Aida, Y. A Novel Antiviral Target Structure Involved in the RNA Binding, Dimerization, and Nuclear Export Functions of the Influenza A Virus Nucleoprotein. PLoS Pathog. 11(7), e1005062 (2015). [PubMed] doi: 10.1371/journal.ppat.1005062.

Sakamaki, K., Imai, K., Tomii, K. & Miller, D.J. Evolutionary analyses of caspase-8 and its paralogs: Deep origins of the apoptotic signaling pathways. BioEssays 37(7), 767-776 (2015). [PubMed] doi: 10.1002/bies.201500010.

Fukasawa, Y., Tsuji, J., Fu, S.C., Tomii, K., Horton, P. & Imai, K. MitoFates: improved prediction of mitochondrial targeting sequences and their cleavage sites. Mol. Cell. Proteomics 14(4), 1113-1126 (2015). [PubMed] doi: 10.1074/mcp.M114.043083.

Santos, H., Imai, K., Makiuchi, T., Tomii, K., Horton, P., Nozawa, A., Ibrahim, M., Tozawa, Y. & Nozaki, T. A novel Mitosomal β-barrel Outer Membrane Protein in Entamoeba. Sci. Rep. 5, 8545 (2015). [PubMed] doi: 10.1038/srep08545.

Ito, J., Ikeda, K., Yamada, K., Mizuguchi, K. & Tomii, K. PoSSuM v.2.0: data update and a new function for investigating ligand analogs and target proteins of small-molecule drugs. Nucleic Acids Res. 43(Database issue), D392-398 (2015). [PubMed] doi: 10.1093/nar/gku1144.

Nagano, N., Nakayama, N., Ikeda, K., Fukuie, M., Yokota, K., Doi, T., Kato, T. & Tomii, K. EzCatDB: the enzyme reaction database, 2015 update. Nucleic Acids Res. 43(Database issue), D453-458 (2015). [PubMed] doi: 10.1093/nar/gku946.

Sakamaki, K., Shimizu, K., Iwata, H., Imai, K., Satou, Y., Funayama, N., Nozaki, M., Yajima, M., Nishimura, O., Higuchi, M., Chiba, K., Yoshimoto, M., Kimura, H. Gracey, A.Y., Shimizu, T., Tomii, K., Goto, O., Akasaka, K., Sawasaki, T. & Miller, D.J. The apoptotic initiator caspase-8: its functional ubiquity and genetic diversity during animal evolution. Mol. Biol. Evol. 31(12), 3282-3301 (2014). [PubMed] doi: 10.1093/molbev/msu260.

Fu, S.C., Imai, K., Sawasaki, T. & Tomii, K. ScreenCap3: Improving prediction of caspase-3 cleavage sites using experimentally verified noncleavage sites. Proteomics. 14(17-18), 2042-2046 (2014). [PubMed] doi: 10.1002/pmic.201400002.

Marumo, K., Nakada-Tsukui, K., Tomii, K. & Nozaki, T. Ligand heterogeneity of the cysteine protease binding protein family in the parasitic protist Entamoeba histolytica. Int. J. Parasitol. 44(9), 625-635 (2014). [PubMed] doi: 10.1016/j.ijpara.2014.04.008.

Yamada, K. & Tomii, K. Revisiting amino acid substitution matrices for identifying distantly related proteins. Bioinformatics. 30(3), 317-325 (2014). [PubMed] doi: 10.1093/bioinformatics/btt694.

Tamura, Y., Harada, Y., Nishikawa, S., Yamano, K., Kamiya, M., Shiota, T., Kuroda, T., Kuge, O., Sesaki, H., Imai, K., Tomii, K. & Endo, T. Tam41 is a CDP-diacylglycerol synthase required for cardiolipin biosynthesis in mitochondria. Cell Metabolism. 17(5), 709-718 (2013). [PubMed] doi: 10.1016/j.cmet.2013.03.018.

Nishino, T., Rago, F., Hori, T., Tomii, K., Cheeseman, I.M. & Fukagawa, T. CENP-T provides a structural platform for outer kinetochore assembly. EMBO J. 32(3), 424-436 (2013). [PubMed] doi: 10.1038/emboj.2012.348.

Kimura, M., Kose, S., Okumura, N., Imai, K., Furuta, M., Sakiyama, N., Tomii, K., Horton, P., Takao, T. & Imamoto N. Identification of cargo proteins specific for the nucleocytoplasmic transport carrier transportin by combination of an in vitro transport system and SILAC-based quantitative proteomics. Mol. Cell. Proteomics 12(1), 145-157 (2013). [PubMed] doi: 10.1074/mcp.M112.019414.

Tsuji, J., Frith, M.C., Tomii, K. & Horton, P. Mammalian NUMT insertion is non-random. Nucleic Acids Res. 40(18), 9073-9088 (2012). [PubMed] doi: 10.1093/nar/gks424.

Tomii, K., Sawada, Y. & Honda, S. Convergent evolution in structural elements of proteins investigated using cross profile analysis. BMC Bioinformatics 13, 11 (2012). [PubMed] doi: 10.1186/1471-2105-13-11.

Ito, J., Tabei, Y., Shimizu, K., Tsuda, K. & Tomii, K. PoSSuM: a database of similar protein-ligand binding and putative pockets. Nucleic Acids Res. 40(Database issue), D541-D548 (2012). [PubMed] doi: 10.1093/nar/gkr1130.

Ito, J., Tabei, Y., Shimizu, K., Tomii, K. & Tsuda, K. PDB-scale analysis of known and putative ligand-binding sites with structural sketches. Proteins. 80(3), 747-763 (2012). [PubMed] doi: 10.1002/prot.23232.

Mukai, Y., Yoshizawa, M., Sasaki, T., Ikeda, M., Tomii, K., Hirokawa, T. & Suwa, M. Discrimination of Golgi type II membrane proteins based on their hydropathy profiles and the amino acid propensities of their transmembrane regions. Biosci. Biotechnol. Biochem. 75(1), 82-88 (2011). [PubMed] doi: 10.1271/bbb.100571.

Motono, C., Nakata, J., Koike, R., Shimizu, K., Shirota, M., Amemiya, T., Tomii, K., Nagano, N., Sakaya, N., Misoo, K., Sato, M., Kidera, A., Hiroaki, H., Shirai, T., Kinoshita, K., Noguchi, T. & Ota, M. SAHG, a comprehensive database of predicted structures of all human proteins. Nucleic Acids Res. 39(Database issue), D487-D493 (2011). [PubMed] doi: 10.1093/nar/gkq1057.

Ito, J., Sonobe, Y., Ikeda, K., Tomii, K. & Higo, J. Universal partitioning of the hierarchical fold network of 50-residue segments in proteins. BMC Structural Biology 9, 34 (2009). [PubMed] doi: 10.1186/1472-6807-9-34.

Ikeda, K., Hirokawa, T., Higo, J. & Tomii, K. Protein-segement universe exhibiting transitions at intermediate segment length in conformational subspaces. BMC Structural Biology 8, 37 (2008). [PubMed] doi: 10.1186/1472-6807-8-37.

Shimizu, K., Muraoka, Y., Hirose, S., Tomii, K. & Noguchi, T. Predicting mostly disordered proteins by using structure-unknown protein data. BMC Bioinformatics 8, 78 (2007). [PubMed] doi: 10.1186/1471-2105-8-78.

Iwaya, N., Goda, N., Fujiwara, K., Tanaka, T., Tomii, K., Tochio, H., Shirakawa, M. & Hiroaki, H. Fine-tuning of protein domain boundary by minimizing potential coiled coil regions. J. Biomol. NMR 37(1), 53-63 (2007). [PubMed] doi: 10.1007/s10858-006-9103-0.

Tomii, K., Hirokawa, T. & Motono, C. Protein structure prediction using a variety of profile libraries and 3D verification. Proteins 61 Suppl. 7, 114-121 (2005). [PubMed] doi: 10.1002/prot.20727.

Ikeda, K., Tomii, K., Yokomizo, T., Mitomo, D., Maruyama, K., Suzuki, S. & Higo, J. Visualization of conformational distribution of short to medium size segments in globular proteins and identification of local structural motifs. Protein Sci. 14(15), 1253-1265 (2005). [PubMed] doi: 10.1110/ps.04956305.

Suenaga, A., Takada, N., Hatakeyama, M., Ichikawa, M., Yu, X., Tomii, K., Okimoto, N., Futatsugi, N., Narumi, T., Shirouzu, M., Yokoyama, S., Konagaya, A. & Taiji, M. Novel mechanism of interaction of p85 subunit of phosphatidylinositol 3-kinase and ErbB3 receptor-derived phosphotyrosyl peptides. J. Biol. Chem. 280(2), 1321-1326 (2005). [PubMed] doi: 10.1074/jbc.M410436200.

Shiozawa, K., Maita, N., Tomii, K., Seto, A., Goda, N., Akiyama, Y., Shimizu, T., Shirakawa, M. & Hiroaki, H. Crystallographic characterization of the N-terminal domain of PEX1. Acta Crystallogr. D Biol. Crystallogr. 60(Pt 11), 2098-2099 (2004). [PubMed] doi: 10.1107/S090744490402428X.

Shiozawa, K., Maita, N., Tomii, K., Seto, A., Goda, N., Akiyama, Y., Shimizu, T., Shirakawa, M. & Hiroaki, H. Structure of the N-terminal domain of PEX1 AAA-ATPase. Characterization of a putative adaptor-binding domain. J. Biol. Chem. 279(48), 50060-50068 (2004). [PubMed] doi: 10.1074/jbc.M407837200.

Tomii, K. & Akiyama, Y. FORTE: a profile-profile comparison tool for protein fold recognition. Bioinformatics. 20(4), 594-595 (2004). [PubMed] doi: 10.1093/bioinformatics/btg474.

Tomii, K. & Kanehisa, M. A comparative analysis of ABC transporters in complete microbial genomes. Genome Res. 8(10), 1048-1059 (1998). [PubMed] doi: 10.1101/gr.8.10.1048.

Tomii, K. & Kanehisa, M. Analysis of amino acid indices and mutation matrices for sequence comparison and structure prediction of proteins. Protein Eng. 9(1), 27-36 (1996). [PubMed] doi: 10.1093/protein/9.1.27.

Book Chapters

Tsuchiya, Y. & Tomii, K. Structural Modeling and Ligand-Binding Prediction for Analysis of Structure-Unknown and Function-Unknown Proteins Using FORTE Alignment and PoSSuM Pocket Search. Methods in Molecular Biology 2165, 1-11 (2020). [PubMed] doi: 10.1007/978-1-0716-0708-4_1.

Tomii, K. Protein Properties. Reference Module in Life Sciences, Encyclopedia of Bioinformatics and Computational Biology, 2, 28-33 (2019). [ScienceDirect] doi: 10.1016/B978-0-12-809633-8.20266-5.

Tomii, K. & Yamada, K. Systematic Exploration of an Efficient Amino Acid Substitution Matrix: MIQS. Methods in Molecular Biology 1415, 211-223 (2016). [PubMed] doi: 10.1007/978-1-4939-3572-7_11.

Imai, K., Hayat, S., Sakiyama, N., Fujita, N., Tomii, K., Elofsson, A. & Horton, P. Localization prediction and structure-based in silico analysis of bacterial proteins: with emphasis on outer membrane proteins. Methods in Molecular Biology 939, 115-140 (2013). [PubMed] doi: 10.1007/978-1-62703-107-3_10.

Kato, T., Tsuda, K., Tomii, K. & Asai, K. A New Variational Framework for Rigid-Body Alignment. In Fred, A., Caelli, T., Duin, R.P.W., Campilho, A. & Ridder, D. (eds), Structural, Syntactic and Statistical Pattern Recognition, Springer, pp. 171-179 (2004). [Springer] doi: 10.1007/b98738.

Tomii, K. & Kanehisa, M. Systematic Detection of Protein Structural Motifs. In Wang, J.T.L., Shapiro, B.A. & Shasha, D. (eds), Pattern Discovery in Biomolecular Data: Tools, Techniques, and Applications, Oxford University Press, Chapter 6, pp. 97-110 (1999). [University Press Scholarship Online]

Tomii, K. & Kanehisa, M. Current status of pathway analysis. Tanpakushitsu Kakusan Koso. 42, 3026-3032 (1997). [Article in Japanese] [PubMed]

Invitations, Presentations

simSAS 2019 – Simulations of Small Angle Scattering for Soft Matter and Life Sciences, Grenoble, France, April 8-11/12, 2019. What went wrong and right in trying to improve models for CASP-SAXS targets? Tomii, K. [simSAS 2019]

CASP13 – 13^th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction, Riviera Maya, Mexico, December 1-4, 2018. SAXS/SANS data assisted modeling Tainer, J., & Tomii, K. [CASP13]

CASP12 – 12^th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction, Gaeta, Italy, December 10-13, 2016. Improved Profile Construction Methods and their Applications to 3D Structure Prediction of Proteins. Oda, T., Nakamura, T., Fukasawa, Y., & Tomii, K. [CASP12]

CAPRI round 30/CASP11 – 11^th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction, Riviera Maya, Mexico, December 7-10, 2014. Homology/Template-based modeling of protein complexes. Tomii, K. [CASP11]

SocBiN – Bioinformatics 2012, Stockholm, Sweden, June 13, 2012. [SocBiN]

Asian Workshop for Protein Structure Prediction Methodology, Seoul, Korea, September 19, 2009. [workshop site]

International Symposium on Multi-Scale Dynamics of Protein Complex Formation and Function, Tokyo, Japan, July 14, 2009. [symposium site]

CASP6 – 6^th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction, Gaeta, Italy, December 4-8, 2004. [CASP6]

ISCBB – International Symposium on Computational Biology and Bioinformatics, Gyeongju, Korea, November 26, 2004. [ISCBB]