Publications

Papers in Pubmed

2011
1:
Community-wide assessment of protein-interface modeling suggests improvements to design methodology.
Fleishman SJ, Whitehead TA, Strauch EM, Corn JE, Qin S, Zhou HX, Mitchell JC, Demerdash ON, Takeda-Shitaka M, Terashi G, Moal IH, Li X, Bates PA, Zacharias M, Park H, Ko JS, Lee H, Seok C, Bourquard T, Bernauer J, Poupon A, Azé J, Soner S, Ovalı SK, Ozbek P, Tal NB, Haliloglu T, Hwang H, Vreven T, Pierce BG, Weng Z, Pérez-Cano L, Pons C, Fernández-Recio J, Jiang F, Yang F, Gong X, Cao L, Xu X, Liu B, Wang P, Li C, Wang C, Robert CH, Guharoy M, Liu S, Huang Y, Li L, Guo D, Chen Y, Xiao Y, London N, Itzhaki Z, Schueler-Furman O, Inbar Y, Potapov V, Cohen M, Schreiber G, Tsuchiya Y, Kanamori E, Standley DM, Nakamura H, Kinoshita K, Driggers CM, Hall RG, Morgan JL, Hsu VL, Zhan J, Yang Y, Zhou Y, Kastritis PL, Bonvin AM, Zhang W, Camacho CJ, Kilambi KP, Sircar A, Gray JJ, Ohue M, Uchikoga N, Matsuzaki Y, Ishida T, Akiyama Y, Khashan R, Bush S, Fouches D, Tropsha A, Esquivel-Rodríguez J, Kihara D, Stranges PB, Jacak R, Kuhlman B, Huang SY, Zou X, Wodak SJ, Janin J, Baker D.
J Mol Biol. 2011 Nov 25;414(2):289-302. Epub 2011 Sep 29.
PMID: 22001016 [PubMed - in process]
Related Articles

Assessing the utility of gene co-expression stability in combination with correlation in the analysis of protein-protein interaction networks

A Patil, K Nakai, K Kinoshita.

BMC Genomics. 2011 Nov 30;12 Suppl 3:S19. Epub 2011 Nov 30.

PMID: 22369639 [PubMed - in process]

Absolute quality evaluation of protein model structures using statistical potentials with respect to the native and reference states.

Shirota M, Ishida K, Kasahara K, Kinoshita K.

Proteins. 2011 May;79(5):1550-63. doi: 10.1002/prot.22982. Epub 2011 Mar 1.

PMID: 21365682 [PubMed - indexed for MEDLINE]

ATTED-II updates: condition-specific gene coexpression to extend coexpression analyses and applications to a broad range of flowering plants.

Obayashi T, Nishida K, Kasahara K, Kinoshita K.

Plant Cell Physiol. 2011 Feb;52(2):213-9. Epub 2011 Jan 7.

PMID: 21217125 [PubMed - indexed for MEDLINE]

COXPRESdb: a database to compare gene coexpression in seven model animals.

Obayashi T, Kinoshita K.

Nucleic Acids Res. 2011 Jan;39(Database issue):D1016-22. Epub 2010 Nov 16.

PMID: 21081562 [PubMed - indexed for MEDLINE]

SAHG, a comprehensive database of predicted structures of all human proteins.

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

Nuclieic Acids Res. 2011 Jan;39(Database issue):D487-93 , Epub 2010 Nov 3.

PMID: 21051360 [PubMed - indexed for MEDLINE]

2010
1:
Similarities and differences in the structure and function of 4.1G and 4.1R135, two protein 4.1 paralogues expressed in erythroid cells.
Kinoshita K, Parra M, Gascard P, An X, Mohandas N, Takakuwa Y.
Biochem J. 2010 Dec 1;432(2):407-16
PMID: 20812914 [PubMed - indexed for MEDLINE]
Related Articles

2:
Domain distribution and intrinsic disorder in hubs in the human protein-protein interaction network.
Patil A, Kinoshita K, Nakamura H.
Protein Sci. 2010 Aug;19(8):1461-8
PMID: 20509167 [PubMed - indexed for MEDLINE]
Related Articles
3:
Correction: patil, a. Et Al. Hub promiscuity in protein-protein interaction networks. Int. J. Mol. Sci. 2010, 11, 1930-1943.
Patil A, Kinoshita K, Nakamura H.
Int J Mol Sci. 2010 Jul 27;11(8):2791.
PMID: 21152273 [PubMed]
Related Articles
4:
Ligand-binding site prediction of proteins based on known fragment-fragment interactions.
Kasahara K, Kinoshita K, Takagi H.
Bioinformatics. 2010 Jun 15;26(12):1493-9. Epub 2010 May 13.
PMID: 20472546 [PubMed - indexed for MEDLINE]
Related Articles
5:
Coexpression landscape in ATTED-II: usage of gene list and gene network for various types of pathways.
Obayashi T, Kinoshita K.
J Plant Res. 2010 May;123(3):311-9, Epub 2010 Apr 10. Review.
PMID: 20383554 [PubMed - indexed for MEDLINE]
Related Articles
6:
Hub promiscuity in protein-protein interaction networks.
Patil A, Kinoshita K, Nakamura H.
Int J Mol Sci. 2010 Apr 26;11(4):1930-43.
PMID: 20480050 [PubMed]
Related Articles

2009

Multi-dimensional correlations for gene coexpression and application to the large-scale data of Arabidopsis.

Kinoshita K, Obayashi T.

Bioinformatics. 2009 Jul 20. [Epub ahead of print]

PMID: 19620096 [PubMed - as supplied by publisher]

Rank of Correlation Coefficient as a Comparable Measure for Biological Significance of Gene Coexpression.

Obayashi T, Kinoshita K.

DNA Res. 2009 Sep 18. [Epub ahead of print]

PMID: 19767600 [PubMed - as supplied by publisher]

Development of a new meta-score for protein structure prediction from seven all-atom distance dependent potentials using support vector regression.

Shirota M, Ishida T, Kinoshita K.

Genome Inform. 2009 Oct;23(1):149-58.

PMID: 20180270 [PubMed - indexed for MEDLINE]

Analyses on hydrophobicity and attractiveness of all-atom distance-dependent potentials.

Shirota M, Ishida T, Kinoshita K.

Protein Sci. 2009 Sep;18(9):1906-15.

PMID: 19588493 [PubMed - in process]

Development of new indices to evaluate protein-protein interfaces: assembling space volume, assembling space distance, and global shape descriptor.

Maeda MH, Kinoshita K.

J Mol Graph Model. 2009 Feb;27(6):706-11. Epub 2008 Nov 8.

PMID: 19110457 [PubMed - indexed for MEDLINE]

[Correlation between structure and function of peptidyl-prolyl isomerase]

Ikura T, Kinoshita K, Ito N.

Tanpakushitsu Kakusan Koso. 2009 Feb;54(2):167-72. Review. Japanese. No abstract available.

PMID: 19205352 [PubMed - indexed for MEDLINE]

Classification of heterodimer interfaces using docking models and construction of scoring functions for the complex structure prediction.

Tsuchiya Y, Kanamori E, Nakamura H, Kinoshita K..

Adv Appl Bioinform Chem. 2009;2:79-100. Epub 2009 Sep 22

PMID: 21918618 [PubMed - in process]

ATTED-II provides coexpressed gene networks for Arabidopsis.

Obayashi T, Hayashi S, Saeki M, Ohta H, Kinoshita K.

Nucleic Acids Res. 2009 Jan;37(Database issue):D987-91. Epub 2008 Oct 25.

PMID: 18953027 [PubMed - indexed for MEDLINE]

PiSite: a database of protein interaction sites using multiple binding states in the PDB.

Higurashi M, Ishida T, Kinoshita K.

Nucleic Acids Res. 2009 Jan;37(Database issue):D360-4. Epub 2008 Oct 4.

PMID: 18836195 [PubMed - indexed for MEDLINE]

Before 2008

1:
Development of new indices to evaluate protein-protein interfaces: assembling space volume, assembling space distance, and global shape descriptor.
Maeda MH, Kinoshita K.
J Mol Graph Model. 2009 Feb;27(6):706-11. Epub 2008 Nov 8.
PMID: 19110457 [PubMed - indexed for MEDLINE]
Related Articles
2:
ATTED-II provides coexpressed gene networks for Arabidopsis.
Obayashi T, Hayashi S, Saeki M, Ohta H, Kinoshita K.
Nucleic Acids Res. 2009 Jan;37(Database issue):D987-91. Epub 2008 Oct 25.
PMID: 18953027 [PubMed - indexed for MEDLINE]
Related Articles Free article in PMC | at journal site
3:
PiSite: a database of protein interaction sites using multiple binding states in the PDB.
Higurashi M, Ishida T, Kinoshita K.
Nucleic Acids Res. 2009 Jan;37(Database issue):D360-4. Epub 2008 Oct 4.
PMID: 18836195 [PubMed - indexed for MEDLINE]
Related Articles Free article in PMC | at journal site
4:
Mutational analysis of block and facilitation of HERG current by a class III anti-arrhythmic agent, nifekalant.
Hosaka Y, Iwata M, Kamiya N, Yamada M, Kinoshita K, Fukunishi Y, Tsujimae K, Hibino H, Aizawa Y, Inanobe A, Nakamura H, Kurachi Y.
Channels (Austin). 2007 May-Jun;1(3):198-208. Epub 2007 Jul 6.
PMID: 18690032 [PubMed - indexed for MEDLINE]
Related Articles
5:
Effects of surface-to-volume ratio of proteins on hydrophilic residues: decrease in occurrence and increase in buried fraction.
Shirota M, Ishida T, Kinoshita K.
Protein Sci. 2008 Sep;17(9):1596-602. Epub 2008 Jun 12.
PMID: 18556475 [PubMed - indexed for MEDLINE]
Related Articles Free article in PMC | at journal site
6:
Protein structure databases with new web services for structural biology and biomedical research.
Standley DM, Kinjo AR, Kinoshita K, Nakamura H.
Brief Bioinform. 2008 Jul;9(4):276-85. Epub 2008 Apr 22. Review.
PMID: 18430752 [PubMed - indexed for MEDLINE]
Related Articles
7:
Prediction of disordered regions in proteins based on the meta approach.
Ishida T, Kinoshita K.
Bioinformatics. 2008 Jun 1;24(11):1344-8. Epub 2008 Apr 20.
PMID: 18426805 [PubMed - indexed for MEDLINE]
Related Articles Free article at journal site
8:
Weak correlation between sequence conservation in promoter regions and in protein-coding regions of human-mouse orthologous gene pairs.
Chiba H, Yamashita R, Kinoshita K, Nakai K.
BMC Genomics. 2008 Apr 2;9:152.
PMID: 18384671 [PubMed - indexed for MEDLINE]
Related Articles Free article in PMC | at journal site
9:
A cavity with an appropriate size is the basis of the PPIase activity.
Ikura T, Kinoshita K, Ito N.
Protein Eng Des Sel. 2008 Feb;21(2):83-9. Epub 2008 Jan 5.
PMID: 18175776 [PubMed - indexed for MEDLINE]
Related Articles Free article at journal site
10:
A novel strategy to search conserved transcription factor binding sites among coexpressing genes in human.
Hatanaka Y, Nagasaki M, Yamaguchi R, Obayashi T, Numata K, Fujita A, Shimamura T, Tamada Y, Imoto S, Kinoshita K, Nakai K, Miyano S.
Genome Inform. 2008;20:212-21.
PMID: 19425135 [PubMed - indexed for MEDLINE]
Related Articles Free article at journal site
11:
Identification of transient hub proteins and the possible structural basis for their multiple interactions.
Higurashi M, Ishida T, Kinoshita K.
Protein Sci. 2008 Jan;17(1):72-8.
PMID: 18156468 [PubMed - indexed for MEDLINE]
Related Articles Free article in PMC | at journal site
12:
COXPRESdb: a database of coexpressed gene networks in mammals.
Obayashi T, Hayashi S, Shibaoka M, Saeki M, Ohta H, Kinoshita K.
Nucleic Acids Res. 2008 Jan;36(Database issue):D77-82. Epub 2007 Oct 11.
PMID: 17932064 [PubMed - indexed for MEDLINE]
Related Articles Free article in PMC | at journal site
13:
Docking of protein molecular surfaces with evolutionary trace analysis.
Kanamori E, Murakami Y, Tsuchiya Y, Standley DM, Nakamura H, Kinoshita K.
Proteins. 2007 Dec 1;69(4):832-8.
PMID: 17803239 [PubMed - indexed for MEDLINE]
Related Articles
14:
eF-seek: prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape.
Kinoshita K, Murakami Y, Nakamura H.
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W398-402. Epub 2007 Jun 12.
PMID: 17567616 [PubMed - indexed for MEDLINE]
Related Articles Free article in PMC | at journal site
15:
PrDOS: prediction of disordered protein regions from amino acid sequence.
Ishida T, Kinoshita K.
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W460-4. Epub 2007 Jun 12.
PMID: 17567614 [PubMed - indexed for MEDLINE]
Related Articles Free article in PMC | at journal site
16:
Probabilistic alignment detects remote homology in a pair of protein sequences without homologous sequence information.
Koike R, Kinoshita K, Kidera A.
Proteins. 2007 Feb 15;66(3):655-63.
PMID: 17152080 [PubMed - indexed for MEDLINE]
Related Articles
17:
ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis.
Obayashi T, Kinoshita K, Nakai K, Shibaoka M, Hayashi S, Saeki M, Shibata D, Saito K, Ohta H.
Nucleic Acids Res. 2007 Jan;35(Database issue):D863-9. Epub 2006 Nov 27.
PMID: 17130150 [PubMed - indexed for MEDLINE]
Related Articles Free article in PMC | at journal site
18:
PreBI: prediction of biological interfaces of proteins in crystals.
Tsuchiya Y, Kinoshita K, Ito N, Nakamura H.
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W320-4.
PMID: 16844993 [PubMed - indexed for MEDLINE]
Related Articles Free article in PMC | at journal site
19:
Analyses of homo-oligomer interfaces of proteins from the complementarity of molecular surface, electrostatic potential and hydrophobicity.
Tsuchiya Y, Kinoshita K, Nakamura H.
Protein Eng Des Sel. 2006 Sep;19(9):421-9. Epub 2006 Jul 12.
PMID: 16837482 [PubMed - indexed for MEDLINE]
Related Articles Free article at journal site
20:
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.
Kinoshita K, Kusunoki M, Miyai K.
Endocr J. 2006 Feb;53(1):51-8.
PMID: 16543672 [PubMed - indexed for MEDLINE]
Related Articles Free article at journal site
21:
DBTGR: a database of tunicate promoters and their regulatory elements.
Sierro N, Kusakabe T, Park KJ, Yamashita R, Kinoshita K, Nakai K.
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D552-5.
PMID: 16381930 [PubMed - indexed for MEDLINE]
Related Articles Free article in PMC | at journal site
22:
P-cats: prediction of catalytic residues in proteins from their tertiary structures.
Kinoshita K, Ota M.
Bioinformatics. 2005 Sep 1;21(17):3570-1. Epub 2005 Jun 30.
PMID: 15994193 [PubMed - indexed for MEDLINE]
Related Articles Free article at journal site
23:
Identification of the ligand binding sites on the molecular surface of proteins.
Kinoshita K, Nakamura H.
Protein Sci. 2005 Mar;14(3):711-8. Epub 2005 Feb 2.
PMID: 15689509 [PubMed - indexed for MEDLINE]
Related Articles Free article in PMC | at journal site
24:
PreDs: a server for predicting dsDNA-binding site on protein molecular surfaces.
Tsuchiya Y, Kinoshita K, Nakamura H.
Bioinformatics. 2005 Apr 15;21(8):1721-3. Epub 2004 Dec 21.
PMID: 15613393 [PubMed - indexed for MEDLINE]
Related Articles Free article at journal site
25:
Solution structure of the RWD domain of the mouse GCN2 protein.
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, Yokoyama S.
Protein Sci. 2004 Aug;13(8):2089-100.
PMID: 15273307 [PubMed - indexed for MEDLINE]
Related Articles Free article in PMC | at journal site
26:
Probabilistic description of protein alignments for sequences and structures.
Koike R, Kinoshita K, Kidera A.
Proteins. 2004 Jul 1;56(1):157-66.
PMID: 15162495 [PubMed - indexed for MEDLINE]
Related Articles
27:
Structure-based prediction of DNA-binding sites on proteins using the empirical preference of electrostatic potential and the shape of molecular surfaces.
Tsuchiya Y, Kinoshita K, Nakamura H.
Proteins. 2004 Jun 1;55(4):885-94.
PMID: 15146487 [PubMed - indexed for MEDLINE]
Related Articles
28:
eF-site and PDBjViewer: database and viewer for protein functional sites.
Kinoshita K, Nakamura H.
Bioinformatics. 2004 May 22;20(8):1329-30. Epub 2004 Feb 10.
PMID: 14871866 [PubMed - indexed for MEDLINE]
Related Articles Free article at journal site
29:
Finding evolutionary relations beyond superfamilies: fold-based superfamilies.
Matsuda K, Nishioka T, Kinoshita K, Kawabata T, Go N.
Protein Sci. 2003 Oct;12(10):2239-51.
PMID: 14500881 [PubMed - indexed for MEDLINE]
Related Articles Free article in PMC | at journal site
30:
Crystal structure of the conserved protein TT1542 from Thermus thermophilus HB8.
Handa N, Terada T, Kamewari Y, Hamana H, Tame JR, Park SY, Kinoshita K, Ota M, Nakamura H, Kuramitsu S, Shirouzu M, Yokoyama S.
Protein Sci. 2003 Aug;12(8):1621-32.
PMID: 12876312 [PubMed - indexed for MEDLINE]
Related Articles Free article in PMC | at journal site
31:
Identification of protein biochemical functions by similarity search using the molecular surface database eF-site.
Kinoshita K, Nakamura H.
Protein Sci. 2003 Aug;12(8):1589-95.
PMID: 12876308 [PubMed - indexed for MEDLINE]
Related Articles Free article in PMC | at journal site
32:
Identification of protein functions from a molecular surface database, eF-site.
Kinoshita K, Furui J, Nakamura H.
J Struct Funct Genomics. 2002;2(1):9-22.
PMID: 12836670 [PubMed - indexed for MEDLINE]
Related Articles
33:
Protein informatics towards function identification.
Kinoshita K, Nakamura H.
Curr Opin Struct Biol. 2003 Jun;13(3):396-400. Review.
PMID: 12831893 [PubMed - indexed for MEDLINE]
Related Articles
34:
Prediction of catalytic residues in enzymes based on known tertiary structure, stability profile, and sequence conservation.
Ota M, Kinoshita K, Nishikawa K.
J Mol Biol. 2003 Apr 11;327(5):1053-64.
PMID: 12662930 [PubMed - indexed for MEDLINE]
Related Articles
35:
Ring and zipper formation is the key to understanding the structural variety in all-beta proteins.
Koike R, Kinoshita K, Kidera A.
FEBS Lett. 2003 Jan 2;533(1-3):9-13.
PMID: 12505150 [PubMed - indexed for MEDLINE]
Related Articles
36:
Key amino acid residues required for aryl migration catalysed by the cytochrome P450 2-hydroxyisoflavanone synthase.
Sawada Y, Kinoshita K, Akashi T, Aoki T, Ayabe S.
Plant J. 2002 Sep;31(5):555-64.
PMID: 12207646 [PubMed - indexed for MEDLINE]
Related Articles
37:
[Insight into the relation between protein structure and function]
Kinoshita K.
Tanpakushitsu Kakusan Koso. 2002 Jun;47(8 Suppl):1064-70. Review. Japanese. No abstract available.
PMID: 12099024 [PubMed - indexed for MEDLINE]
Related Articles
38:
Intramolecular interaction of SUR2 subtypes for intracellular ADP-Induced differential control of K(ATP) channels.
Matsushita K, Kinoshita K, Matsuoka T, Fujita A, Fujikado T, Tano Y, Nakamura H, Kurachi Y.
Circ Res. 2002 Mar 22;90(5):554-61.
PMID: 11909819 [PubMed - indexed for MEDLINE]
Related Articles Free article at journal site
39:
Two basic residues, Lys-107 and Lys-118, of RuvC resolvase are involved in critical contacts with the Holliday junction for its resolution.
Yoshikawa M, Iwasaki H, Kinoshita K, Shinagawa H.
Genes Cells. 2000 Oct;5(10):803-13.
PMID: 11029656 [PubMed - indexed for MEDLINE]
Related Articles
40:
Diversity of functions of proteins with internal symmetry in spatial arrangement of secondary structural elements.
Kinoshita K, Kidera A, Go N.
Protein Sci. 1999 Jun;8(6):1210-7.
PMID: 10386871 [PubMed - indexed for MEDLINE]
Related Articles Free article in PMC | at journal site
41:
Structural motif of phosphate-binding site common to various protein superfamilies: all-against-all structural comparison of protein-mononucleotide complexes.
Kinoshita K, Sadanami K, Kidera A, Go N.
Protein Eng. 1999 Jan;12(1):11-4.
PMID: 10065705 [PubMed - indexed for MEDLINE]
Related Articles Free article at journal site

Other publications that are not appeared in Pubmed will be added sooner or later.

Comments

	このサイトを検索