Akira R Kinjo

Akira R Kinjo

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Akira R Kinjo

Publications by authors named "Akira R Kinjo"

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Cooperative "folding transition" in the sequence space facilitates function-driven evolution of protein families.

Authors:
Akira R Kinjo

J Theor Biol 2018 04 31;443:18-27. Epub 2018 Jan 31.

Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.jtbi.2018.01.019DOI Listing
April 2018

Mechanism of evolution by genetic assimilation : Equivalence and independence of genetic mutation and epigenetic modulation in phenotypic expression.

Biophys Rev 2018 Apr 21;10(2):667-676. Epub 2018 Feb 21.

Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.

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http://dx.doi.org/10.1007/s12551-018-0403-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5899745PMC
April 2018

A new look at an old view of denaturant induced protein unfolding.

Anal Biochem 2018 02 21;542:40-57. Epub 2017 Nov 21.

Institute for Protein Research, Osaka University, 3-1- Yamada-oka, Suita, Osaka 565-0871, Japan.

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http://dx.doi.org/10.1016/j.ab.2017.11.011DOI Listing
February 2018

Neuro-symbolic representation learning on biological knowledge graphs.

Bioinformatics 2017 Sep;33(17):2723-2730

Computer, Electrical and Mathematical Sciences & Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia.

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http://dx.doi.org/10.1093/bioinformatics/btx275DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5860058PMC
September 2017

Monte Carlo simulation of a statistical mechanical model of multiple protein sequence alignment.

Authors:
Akira R Kinjo

Biophys Physicobiol 2017 12;14:99-110. Epub 2017 Jul 12.

Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan.

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http://dx.doi.org/10.2142/biophysico.14.0_99DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5551269PMC
July 2017

Essential role of long non-coding RNAs in de novo chromatin modifications: the genomic address code hypothesis.

Biophys Rev 2017 Apr 21;9(2):73-77. Epub 2017 Mar 21.

Institute for Protein Research, Osaka University, Suita, Osaka 565-0871 Japan.

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http://dx.doi.org/10.1007/s12551-017-0259-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5380698PMC
April 2017

Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures.

Nucleic Acids Res 2017 01 26;45(D1):D282-D288. Epub 2016 Oct 26.

Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.

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http://dx.doi.org/10.1093/nar/gkw962DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5210648PMC
January 2017

GIRAF: a method for fast search and flexible alignment of ligand binding interfaces in proteins at atomic resolution.

Biophysics (Nagoya-shi) 2012 31;8:79-94. Epub 2012 May 31.

Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan.

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http://dx.doi.org/10.2142/biophysics.8.79DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4629647PMC
August 2016

Cooperation between phenotypic plasticity and genetic mutations can account for the cumulative selection in evolution.

Biophysics (Nagoya-shi) 2014 17;10:99-108. Epub 2014 Dec 17.

Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.

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http://dx.doi.org/10.2142/biophysics.10.99DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4629657PMC
August 2016

Liquid-theory analogy of direct-coupling analysis of multiple-sequence alignment and its implications for protein structure prediction.

Authors:
Akira R Kinjo

Biophys Physicobiol 2015 11;12:117-9. Epub 2015 Dec 11.

Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan.

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http://dx.doi.org/10.2142/biophysico.12.0_117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4736835PMC
August 2016

Molmil: a molecular viewer for the PDB and beyond.

J Cheminform 2016 26;8(1):42. Epub 2016 Aug 26.

Laboratory of Protein Informatics, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 Japan.

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http://dx.doi.org/10.1186/s13321-016-0155-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5002144PMC
August 2016

A unified statistical model of protein multiple sequence alignment integrating direct coupling and insertions.

Authors:
Akira R Kinjo

Biophys Physicobiol 2016 22;13:45-62. Epub 2016 Apr 22.

Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan.

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http://dx.doi.org/10.2142/biophysico.13.0_45DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5042171PMC
April 2016

Implementation of linked data in the life sciences at BioHackathon 2011.

J Biomed Semantics 2015 7;6. Epub 2015 Jan 7.

Department of Bioclinical informatics, Tohoku Medical Megabank Organization, Tohoku University, Seiryo-cho 4-1, Aoba-ku, Sendai-shi Miyagi, 980-8575 Japan.

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http://dx.doi.org/10.1186/2041-1480-6-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4429360PMC
May 2015

Rigid-body motions of interacting proteins dominate multispecific binding of ubiquitin in a shape-dependent manner.

Proteins 2014 Jan 31;82(1):77-89. Epub 2013 Aug 31.

Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.

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http://dx.doi.org/10.1002/prot.24371DOI Listing
January 2014

Exhaustive comparison and classification of ligand-binding surfaces in proteins.

Protein Sci 2013 Oct 4;22(10):1379-91. Epub 2013 Sep 4.

Graduate School of Information Sciences, Tohoku University, 6-3-09 Aramaki-aza-aoba, Aoba-ku, Sendai, Miyagi, 982-0036, Japan.

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http://dx.doi.org/10.1002/pro.2329DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3795496PMC
October 2013

Counterbalance of ligand- and self-coupled motions characterizes multispecificity of ubiquitin.

Protein Sci 2013 Feb 17;22(2):168-78. Epub 2012 Dec 17.

Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.

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http://dx.doi.org/10.1002/pro.2195DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3588913PMC
February 2013

Functional structural motifs for protein-ligand, protein-protein, and protein-nucleic acid interactions and their connection to supersecondary structures.

Methods Mol Biol 2013 ;932:295-315

Institute for Protein Research, Osaka University, Osaka, Japan.

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http://dx.doi.org/10.1007/978-1-62703-065-6_18DOI Listing
January 2013

Composite structural motifs of binding sites for delineating biological functions of proteins.

PLoS One 2012 8;7(2):e31437. Epub 2012 Feb 8.

Institute for Protein Research, Osaka University, Suita, Osaka, Japan.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0031437PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3275580PMC
July 2012

Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format.

Nucleic Acids Res 2012 Jan 5;40(Database issue):D453-60. Epub 2011 Oct 5.

Institute for Protein Research and Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan.

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http://dx.doi.org/10.1093/nar/gkr811DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245181PMC
January 2012

Functional characterization of protein domains common to animal viruses and mouse.

BMC Genomics 2011 Nov 30;12 Suppl 3:S21. Epub 2011 Nov 30.

Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.

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http://dx.doi.org/10.1186/1471-2164-12-S3-S21DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3333181PMC
November 2011

Distinct roles of overlapping and non-overlapping regions of hub protein interfaces in recognition of multiple partners.

J Mol Biol 2011 Aug 22;411(3):713-27. Epub 2011 Jun 22.

Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.

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http://dx.doi.org/10.1016/j.jmb.2011.06.027DOI Listing
August 2011

PDBj Mine: design and implementation of relational database interface for Protein Data Bank Japan.

Database (Oxford) 2010 Aug 25;2010:baq021. Epub 2010 Aug 25.

Protein Data Bank Japan, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.

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http://dx.doi.org/10.1093/database/baq021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2997606PMC
August 2010

Geometric similarities of protein-protein interfaces at atomic resolution are only observed within homologous families: an exhaustive structural classification study.

J Mol Biol 2010 Jun 24;399(3):526-40. Epub 2010 Apr 24.

Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.

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http://dx.doi.org/10.1016/j.jmb.2010.04.028DOI Listing
June 2010

SeSAW: balancing sequence and structural information in protein functional mapping.

Bioinformatics 2010 May 17;26(9):1258-9. Epub 2010 Mar 17.

WPI Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, Japan.

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http://dx.doi.org/10.1093/bioinformatics/btq116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2859130PMC
May 2010

Profile conditional random fields for modeling protein families with structural information.

Authors:
Akira R Kinjo

Biophysics (Nagoya-shi) 2009 30;5:37-44. Epub 2009 May 30.

Institute for Protein Research, Osaka University, Suita, Osaka, 565-0871, Japan.

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http://dx.doi.org/10.2142/biophysics.5.37DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5036637PMC
May 2009

Comprehensive structural classification of ligand-binding motifs in proteins.

Structure 2009 Feb;17(2):234-46

Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.

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http://dx.doi.org/10.1016/j.str.2008.11.009DOI Listing
February 2009

Protein structure databases with new web services for structural biology and biomedical research.

Brief Bioinform 2008 Jul 22;9(4):276-85. Epub 2008 Apr 22.

Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan.

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http://dx.doi.org/10.1093/bib/bbn015DOI Listing
July 2008

Properties of contact matrices induced by pairwise interactions in proteins.

Phys Rev E Stat Nonlin Soft Matter Phys 2008 May 14;77(5 Pt 1):051910. Epub 2008 May 14.

Graduate School of Engineering, Gunma University, Kiryu, Gunma 376-8515, Japan.

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http://dx.doi.org/10.1103/PhysRevE.77.051910DOI Listing
May 2008

Similarity search for local protein structures at atomic resolution by exploiting a database management system.

Biophysics (Nagoya-shi) 2007 28;3:75-84. Epub 2007 Dec 28.

Institute for Protein Research, Osaka University, Suita, Osaka, 565-0871, Japan.

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http://dx.doi.org/10.2142/biophysics.3.75DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5036654PMC
December 2007

Wang-Landau molecular dynamics technique to search for low-energy conformational space of proteins.

Phys Rev E Stat Nonlin Soft Matter Phys 2007 Jun 27;75(6 Pt 2):066706. Epub 2007 Jun 27.

Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima 411-8540, Japan.

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http://dx.doi.org/10.1103/PhysRevE.75.066706DOI Listing
June 2007

[Protein secondary structure prediction].

Authors:
Akira R Kinjo

Tanpakushitsu Kakusan Koso 2007 Jan;52(1):50-6

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January 2007

CRNPRED: highly accurate prediction of one-dimensional protein structures by large-scale critical random networks.

BMC Bioinformatics 2006 Sep 5;7:401. Epub 2006 Sep 5.

Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, 411-8540, Japan.

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http://dx.doi.org/10.1186/1471-2105-7-401DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1578593PMC
September 2006

Human transcription factors contain a high fraction of intrinsically disordered regions essential for transcriptional regulation.

J Mol Biol 2006 Jun 25;359(4):1137-49. Epub 2006 Apr 25.

Laboratory of Gene-Product Informatics, Center For Information Biology & DNA Data Bank of Japan, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan.

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http://dx.doi.org/10.1016/j.jmb.2006.04.016DOI Listing
June 2006

Predicting secondary structures, contact numbers, and residue-wise contact orders of native protein structures from amino acid sequences using critical random networks.

Biophysics (Nagoya-shi) 2005 22;1:67-74. Epub 2005 Nov 22.

Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima 411-8540, Japan; Department of Genetics, The Graduate University for Advanced Studies (SOKENDAI), Mishima 411-8540, Japan.

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http://dx.doi.org/10.2142/biophysics.1.67DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5036631PMC
November 2005

Recoverable one-dimensional encoding of three-dimensional protein structures.

Bioinformatics 2005 May 18;21(10):2167-70. Epub 2005 Feb 18.

Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima 411-8540, Japan.

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http://dx.doi.org/10.1093/bioinformatics/bti330DOI Listing
May 2005

Predicting absolute contact numbers of native protein structure from amino acid sequence.

Proteins 2005 Jan;58(1):158-65

Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Japan.

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http://dx.doi.org/10.1002/prot.20300DOI Listing
January 2005

Eigenvalue analysis of amino acid substitution matrices reveals a sharp transition of the mode of sequence conservation in proteins.

Bioinformatics 2004 Nov 6;20(16):2504-8. Epub 2004 May 6.

Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, 411-8540, Japan.

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http://dx.doi.org/10.1093/bioinformatics/bth297DOI Listing
November 2004

Competition between protein folding and aggregation with molecular chaperones in crowded solutions: insight from mesoscopic simulations.

Biophys J 2003 Dec;85(6):3521-31

PRESTO, Japan Science and Technology Corporation, Kobe University, Kobe, Japan.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1303659PMC
http://dx.doi.org/10.1016/S0006-3495(03)74772-9DOI Listing
December 2003

Effects of macromolecular crowding on protein folding and aggregation studied by density functional theory: dynamics.

Phys Rev E Stat Nonlin Soft Matter Phys 2002 Nov 7;66(5 Pt 1):051902. Epub 2002 Nov 7.

PRESTO, Japan Science and Technology Corporation, Kobe University, Japan.

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http://dx.doi.org/10.1103/PhysRevE.66.051902DOI Listing
November 2002

Effects of macromolecular crowding on protein folding and aggregation studied by density functional theory: statics.

Phys Rev E Stat Nonlin Soft Matter Phys 2002 Sep 24;66(3 Pt 1):031911. Epub 2002 Sep 24.

PRESTO, Japan Science and Technology Corporation, Kobe University, Kobe 675-8501, Japan.

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http://dx.doi.org/10.1103/PhysRevE.66.031911DOI Listing
September 2002