Papers in Pubmed (before 2008)

• Maeda MH and Kinoshita K. Development of new indices to evaluate protein-protein interfaces: assembling space volume, assembling space distance, and global shape descriptor. J Mol Graph Model, 2009 Feb;27(6):706-11 PubMed Journal
• Obayashi T, Hayashi S, Saeki M, Ohta H and Kinoshita K. ATTED-II provides coexpressed gene networks for Arabidopsis. Nucleic Acids Res, 2009 Jan;37(Database issue):D987-91 PubMed Journal
• Higurashi M, Ishida T and Kinoshita K. PiSite: a database of protein interaction sites using multiple binding states in the PDB. Nucleic Acids Res, 2009 Jan;37(Database issue):D360-4 PubMed Journal
• Hosaka Y, Iwata M, Kamiya N, Yamada M, Kinoshita K, Fukunishi Y, Tsujimae K, Hibino H, Aizawa Y, Inanobe A, Nakamura H and Kurachi Y. Mutational analysis of block and facilitation of HERG current by a class III anti-arrhythmic agent, nifekalant. Channels (Austin), 2007 May-Jun;1(3):198-208 PubMed
• Shirota M, Ishida T and Kinoshita K. Effects of surface-to-volume ratio of proteins on hydrophilic residues: decrease in occurrence and increase in buried fraction. Protein Sci, 2008 Sep;17(9):1596-602 PubMed Journal
• Standley DM, Kinjo AR, Kinoshita K and Nakamura H. Protein structure databases with new web services for structural biology and biomedical research. Brief Bioinform, 2008 Jul;9(4):276-85 PubMed Journal
• Ishida T and Kinoshita K. Prediction of disordered regions in proteins based on the meta approach. Bioinformatics, 2008 Jun 1;24(11):1344-8 PubMed Journal
• Chiba H, Yamashita R, Kinoshita K and Nakai K. Weak correlation between sequence conservation in promoter regions and in protein-coding regions of human-mouse orthologous gene pairs. BMC Genomics, 2008 Apr 2;9:152 PubMed Journal
• Ikura T, Kinoshita K and Ito N. A cavity with an appropriate size is the basis of the PPIase activity. Protein Eng Des Sel, 2008 Feb;21(2):83-9 PubMed Journal
• Hatanaka Y, Nagasaki M, Yamaguchi R, Obayashi T, Numata K, Fujita A, Shimamura T, Tamada Y, Imoto S, Kinoshita K, Nakai K and Miyano S. A novel strategy to search conserved transcription factor binding sites among coexpressing genes in human. Genome Inform, 2008;20:212-21 PubMed
• Higurashi M, Ishida T and Kinoshita K. Identification of transient hub proteins and the possible structural basis for their multiple interactions. Protein Sci, 2008 Jan;17(1):72-8 PubMed Journal
• Obayashi T, Hayashi S, Shibaoka M, Saeki M, Ohta H and Kinoshita K. COXPRESdb: a database of coexpressed gene networks in mammals. Nucleic Acids Res, 2008 Jan;36(Database issue):D77-82 PubMed Journal
• Kanamori E, Murakami Y, Tsuchiya Y, Standley DM, Nakamura H and Kinoshita K. Docking of protein molecular surfaces with evolutionary trace analysis. Proteins, 2007 Dec 1;69(4):832-8 PubMed Journal
• Kinoshita K, Murakami Y and Nakamura H. eF-seek: prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape. Nucleic Acids Res, 2007 Jul;35(Web Server issue):W398-402 PubMed Journal
• Ishida T and Kinoshita K. PrDOS: prediction of disordered protein regions from amino acid sequence. Nucleic Acids Res, 2007 Jul;35(Web Server issue):W460-4 PubMed Journal
• Koike R, Kinoshita K and Kidera A. Probabilistic alignment detects remote homology in a pair of protein sequences without homologous sequence information. Proteins, 2007 Feb 15;66(3):655-63 PubMed Journal
• Obayashi T, Kinoshita K, Nakai K, Shibaoka M, Hayashi S, Saeki M, Shibata D, Saito K and Ohta H. ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis. Nucleic Acids Res, 2007 Jan;35(Database issue):D863-9 PubMed Journal
• Tsuchiya Y, Kinoshita K, Ito N and Nakamura H. PreBI: prediction of biological interfaces of proteins in crystals. Nucleic Acids Res, 2006 Jul 1;34(Web Server issue):W320-4 PubMed Journal
• Tsuchiya Y, Kinoshita K and Nakamura H. Analyses of homo-oligomer interfaces of proteins from the complementarity of molecular surface, electrostatic potential and hydrophobicity. Protein Eng Des Sel, 2006 Sep;19(9):421-9 PubMed Journal
• Kinoshita K, Kusunoki M and Miyai K. Analysis of the three dimensional structure of the CXGXC motif in the CMGCC and CAGYC regions of alpha-and beta-subunits of human chorionic gonadotropin: importance of glycine residue (G) in the motif. Endocr J, 2006 Feb;53(1):51-8 PubMed
• Sierro N, Kusakabe T, Park KJ, Yamashita R, Kinoshita K and Nakai K. DBTGR: a database of tunicate promoters and their regulatory elements. Nucleic Acids Res, 2006 Jan 1;34(Database issue):D552-5 PubMed Journal
• Kinoshita K and Ota M. P-cats: prediction of catalytic residues in proteins from their tertiary structures. Bioinformatics, 2005 Sep 1;21(17):3570-1 PubMed Journal
• Kinoshita K and Nakamura H. Identification of the ligand binding sites on the molecular surface of proteins. Protein Sci, 2005 Mar;14(3):711-8 PubMed Journal
• Tsuchiya Y, Kinoshita K and Nakamura H. PreDs: a server for predicting dsDNA-binding site on protein molecular surfaces. Bioinformatics, 2005 Apr 15;21(8):1721-3 PubMed Journal
• Nameki N, Yoneyama M, Koshiba S, Tochio N, Inoue M, Seki E, Matsuda T, Tomo Y, Harada T, Saito K, Kobayashi N, Yabuki T, Aoki M, Nunokawa E, Matsuda N, Sakagami N, Terada T, Shirouzu M, Yoshida M, Hirota H, Osanai T, Tanaka A, Arakawa T, Carninci P, Kawai J, Hayashizaki Y, Kinoshita K, Güntert P, Kigawa T and Yokoyama S. Solution structure of the RWD domain of the mouse GCN2 protein. Protein Sci, 2004 Aug;13(8):2089-100 PubMed Journal
• Koike R, Kinoshita K and Kidera A. Probabilistic description of protein alignments for sequences and structures. Proteins, 2004 Jul 1;56(1):157-66 PubMed Journal
• Tsuchiya Y, Kinoshita K and Nakamura H. Structure-based prediction of DNA-binding sites on proteins using the empirical preference of electrostatic potential and the shape of molecular surfaces. Proteins, 2004 Jun 1;55(4):885-94 PubMed Journal
• Kinoshita K and Nakamura H. eF-site and PDBjViewer: database and viewer for protein functional sites. Bioinformatics, 2004 May 22;20(8):1329-30 PubMed Journal
• Matsuda K, Nishioka T, Kinoshita K, Kawabata T and Go N. Finding evolutionary relations beyond superfamilies: fold-based superfamilies. Protein Sci, 2003 Oct;12(10):2239-51 PubMed Journal
• Handa N, Terada T, Kamewari Y, Hamana H, Tame JR, Park SY, Kinoshita K, Ota M, Nakamura H, Kuramitsu S, Shirouzu M and Yokoyama S. Crystal structure of the conserved protein TT1542 from Thermus thermophilus HB8. Protein Sci, 2003 Aug;12(8):1621-32 PubMed Journal
• Kinoshita K and Nakamura H. Identification of protein biochemical functions by similarity search using the molecular surface database eF-site. Protein Sci, 2003 Aug;12(8):1589-95 PubMed Journal
• Kinoshita K, Furui J and Nakamura H. Identification of protein functions from a molecular surface database, eF-site. J Struct Funct Genomics, 2002;2(1):9-22 PubMed
• Kinoshita K and Nakamura H. Protein informatics towards function identification. Curr Opin Struct Biol, 2003 Jun;13(3):396-400 PubMed
• Ota M, Kinoshita K and Nishikawa K. Prediction of catalytic residues in enzymes based on known tertiary structure, stability profile, and sequence conservation. J Mol Biol, 2003 Apr 11;327(5):1053-64 PubMed
• Koike R, Kinoshita K and Kidera A. Ring and zipper formation is the key to understanding the structural variety in all-beta proteins. FEBS Lett, 2003 Jan 2;533(1-3):9-13 PubMed
• Sawada Y, Kinoshita K, Akashi T, Aoki T and Ayabe S. Key amino acid residues required for aryl migration catalysed by the cytochrome P450 2-hydroxyisoflavanone synthase. Plant J, 2002 Sep;31(5):555-64 PubMed
• Kinoshita K. [Insight into the relation between protein structure and function]. Tanpakushitsu Kakusan Koso, 2002 Jun;47(8 Suppl):1064-70 PubMed
• Matsushita K, Kinoshita K, Matsuoka T, Fujita A, Fujikado T, Tano Y, Nakamura H and Kurachi Y. Intramolecular interaction of SUR2 subtypes for intracellular ADP-Induced differential control of K(ATP) channels. Circ Res, 2002 Mar 22;90(5):554-61 PubMed
• Yoshikawa M, Iwasaki H, Kinoshita K and Shinagawa H. Two basic residues, Lys-107 and Lys-118, of RuvC resolvase are involved in critical contacts with the Holliday junction for its resolution. Genes Cells, 2000 Oct;5(10):803-13 PubMed
• Kinoshita K, Kidera A and Go N. Diversity of functions of proteins with internal symmetry in spatial arrangement of secondary structural elements. Protein Sci, 1999 Jun;8(6):1210-7 PubMed Journal
• Kinoshita K, Sadanami K, Kidera A and Go N. Structural motif of phosphate-binding site common to various protein superfamilies: all-against-all structural comparison of protein-mononucleotide complexes. Protein Eng, 1999 Jan;12(1):11-4 PubMed