Literature DB >> 14871866

eF-site and PDBjViewer: database and viewer for protein functional sites.

Kengo Kinoshita1, Haruki Nakamura.   

Abstract

UNLABELLED: The electrostatic-surface of functional site (eF-site) is a database for the molecular surfaces of protein functional sites. To enable browsing of each molecular surface along with the atomic model, we have developed a new three-dimensional interactive viewer, PDBjViewer, that can be used both as an applet and as a stand-alone program. AVAILABILITY: The eF-site database and PDBjViewer are freely available from http://www.pdbj.org/eF-site/

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Year:  2004        PMID： 14871866     DOI： 10.1093/bioinformatics/bth073

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  52 in total

1.  RabGDIα is a negative regulator of interferon-γ-inducible GTPase-dependent cell-autonomous immunity to Toxoplasma gondii.

Authors:  Jun Ohshima; Miwa Sasai; Jianfa Liu; Kazuo Yamashita; Ji Su Ma; Youngae Lee; Hironori Bando; Jonathan C Howard; Shigeyuki Ebisu; Mikako Hayashi; Kiyoshi Takeda; Daron M Standley; Eva-Maria Frickel; Masahiro Yamamoto
Journal:  Proc Natl Acad Sci U S A       Date:  2015-08-03       Impact factor: 11.205

2.  The diversity of H3 loops determines the antigen-binding tendencies of antibody CDR loops.

Authors:  Yuko Tsuchiya; Kenji Mizuguchi
Journal:  Protein Sci       Date:  2016-01-20       Impact factor: 6.725

3.  Identification of the ligand binding sites on the molecular surface of proteins.

Authors:  Kengo Kinoshita; Haruki Nakamura
Journal:  Protein Sci       Date:  2005-02-02       Impact factor: 6.725

Review 4.  Data deposition and annotation at the worldwide protein data bank.

Authors:  Shuchismita Dutta; Kyle Burkhardt; Jasmine Young; Ganesh J Swaminathan; Takanori Matsuura; Kim Henrick; Haruki Nakamura; Helen M Berman
Journal:  Mol Biotechnol       Date:  2008-12-10       Impact factor: 2.695

5.  Dynamic energy landscape view of coupled binding and protein conformational change: induced-fit versus population-shift mechanisms.

Authors:  Kei-Ichi Okazaki; Shoji Takada
Journal:  Proc Natl Acad Sci U S A       Date:  2008-08-04       Impact factor: 11.205

Review 6.  Exploring the structure and function paradigm.

Authors:  Oliver C Redfern; Benoit Dessailly; Christine A Orengo
Journal:  Curr Opin Struct Biol       Date:  2008-06       Impact factor: 6.809

7.  A mutation in the immunoproteasome subunit PSMB8 causes autoinflammation and lipodystrophy in humans.

Authors:  Akiko Kitamura; Yoichi Maekawa; Hisanori Uehara; Keisuke Izumi; Izumi Kawachi; Masatoyo Nishizawa; Yasuko Toyoshima; Hitoshi Takahashi; Daron M Standley; Keiji Tanaka; Jun Hamazaki; Shigeo Murata; Koji Obara; Itaru Toyoshima; Koji Yasutomo
Journal:  J Clin Invest       Date:  2011-09-01       Impact factor: 14.808

8.  Retinoblastoma-binding Protein 4-regulated Classical Nuclear Transport Is Involved in Cellular Senescence.

Authors:  Akira Tsujii; Yoichi Miyamoto; Tetsuji Moriyama; Yuko Tsuchiya; Chikashi Obuse; Kenji Mizuguchi; Masahiro Oka; Yoshihiro Yoneda
Journal:  J Biol Chem       Date:  2015-10-21       Impact factor: 5.157

Review 9.  Hub promiscuity in protein-protein interaction networks.

Authors:  Ashwini Patil; Kengo Kinoshita; Haruki Nakamura
Journal:  Int J Mol Sci       Date:  2010-04-26       Impact factor: 5.923

10.  FLORA: a novel method to predict protein function from structure in diverse superfamilies.

Authors:  Oliver C Redfern; Benoît H Dessailly; Timothy J Dallman; Ian Sillitoe; Christine A Orengo
Journal:  PLoS Comput Biol       Date:  2009-08-28       Impact factor: 4.475
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