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A. Kinjo · SciRah

Researcher profile · Semantic Scholar

A. Kinjo

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A. Kinjo — researcher profile on SciRah

h-index: 21
Works: 101
Citations: 1,705

Most-cited papers

Human transcription factors contain a high fraction of intrinsically disordered regions essential for transcriptional regulation.
Y. Minezaki, Keiichi Homma, A. Kinjo, K. Nishikawa
2006Journal of Molecular Biology263 citations
Semantic Scholar
Neuro-symbolic representation learning on biological knowledge graphs
M. Alshahrani, Mohammad Asif Khan, Omar Maddouri, A. Kinjo +2 more
2016Bioinform.157 citations Open access
Semantic Scholar
Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format
A. Kinjo, Hirofumi Suzuki, R. Yamashita, Yasuyo Ikegawa +7 more
2011Nucleic Acids Res.134 citations Open access
Semantic Scholar
Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures
A. Kinjo, G. Bekker, Hirofumi Suzuki, Y. Tsuchiya +3 more
2016Nucleic Acids Res.112 citations Open access
Semantic Scholar
New tools and functions in data‐out activities at Protein Data Bank Japan (PDBj)
A. Kinjo, G. Bekker, H. Wako, S. Endo +12 more
2017Protein Science92 citations Open access
Semantic Scholar
Protein structure databases with new web services for structural biology and biomedical research
D. Standley, A. Kinjo, K. Kinoshita, Haruki Nakamura
2008Briefings Bioinform.74 citations Open access
Semantic Scholar
Molmil: a molecular viewer for the PDB and beyond
G. Bekker, Haruki Nakamura, A. Kinjo
2016Journal of Cheminformatics73 citations Open access
Semantic Scholar
Predicting absolute contact numbers of native protein structure from amino acid sequence
A. Kinjo, K. Horimoto, K. Nishikawa
2004Proteins: Structure, Function, and Bioinformatics68 citations
Semantic Scholar
Comprehensive structural classification of ligand-binding motifs in proteins.
A. Kinjo, Haruki Nakamura
2008Structure51 citations Open access
Semantic Scholar
Competition between protein folding and aggregation with molecular chaperones in crowded solutions: insight from mesoscopic simulations.
A. Kinjo, S. Takada
2003Biophysical Journal47 citations Open access
Semantic Scholar
Mechanism of evolution by genetic assimilation
K. Nishikawa, A. Kinjo
2018Biophysical Reviews45 citations Open access
Semantic Scholar
Eigenvalue analysis of amino acid substitution matrices reveals a sharp transition of the mode of sequence conservation in proteins
A. Kinjo, K. Nishikawa
2004Bioinform.41 citations
Semantic Scholar
CRNPRED: highly accurate prediction of one-dimensional protein structures by large-scale critical random networks
A. Kinjo, K. Nishikawa
2006BMC Bioinformatics37 citations Open access
Semantic Scholar
Effects of macromolecular crowding on protein folding and aggregation studied by density functional theory: statics.
A. Kinjo, S. Takada
2002Physical review. E, Statistical, nonlinear, and soft matter physics35 citations
Semantic Scholar
The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies
Toshiaki Katayama, Mark D. Wilkinson, G. Micklem, Shuichi Kawashima +62 more
2013Journal of Biomedical Semantics31 citations Open access
Semantic Scholar
Recoverable one-dimensional encoding of three-dimensional protein structures
A. Kinjo, K. Nishikawa
2005Bioinform.31 citations Open access
Semantic Scholar
The DBCLS BioHackathon : standardization and interoperability for bioinformatics web services and workflows
Toshiaki Katayama, K. Arakawa, Mitsuteru Nakao, K. Aoki-Kinoshita +17 more
201028 citations
Semantic Scholar
Similarity search for local protein structures at atomic resolution by exploiting a database management system
A. Kinjo, Haruki Nakamura
2007Biophysics26 citations Open access
Semantic Scholar
Effects of macromolecular crowding on protein folding and aggregation studied by density functional theory: dynamics.
A. Kinjo, S. Takada
2002Physical review. E, Statistical, nonlinear, and soft matter physics24 citations
Semantic Scholar
Geometric similarities of protein-protein interfaces at atomic resolution are only observed within homologous families: an exhaustive structural classification study.
A. Kinjo, Haruki Nakamura
2010Journal of Molecular Biology23 citations
Semantic Scholar
The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications
Toshiaki Katayama, Mark D. Wilkinson, Rutger A. Vos, T. Kawashima +53 more
2011Journal of Biomedical Semantics21 citations Open access
Semantic Scholar
PDBj Mine: design and implementation of relational database interface for Protein Data Bank Japan
A. Kinjo, R. Yamashita, Haruki Nakamura
2010Database J. Biol. Databases Curation21 citations Open access
Semantic Scholar
Predicting secondary structures, contact numbers, and residue-wise contact orders of native protein structures from amino acid sequences using critical random networks
A. Kinjo, K. Nishikawa
2005Biophysics19 citations Open access
Semantic Scholar
Distinct roles of overlapping and non-overlapping regions of hub protein interfaces in recognition of multiple partners.
B. Dasgupta, Haruki Nakamura, A. Kinjo
2011Journal of Molecular Biology18 citations Open access
Semantic Scholar
Wang-Landau molecular dynamics technique to search for low-energy conformational space of proteins.
T. Nagasima, A. Kinjo, Takashi Mitsui, K. Nishikawa
2007Physical review. E, Statistical, nonlinear, and soft matter physics18 citations Open access
Semantic Scholar
Implementation of linked data in the life sciences at BioHackathon 2011
K. Aoki-Kinoshita, A. Kinjo, Mizuki Morita, Yoshinobu Igarashi +12 more
2015Journal of Biomedical Semantics17 citations Open access
Semantic Scholar
Essential role of long non-coding RNAs in de novo chromatin modifications: the genomic address code hypothesis
K. Nishikawa, A. Kinjo
2017Biophysical Reviews15 citations Open access
Semantic Scholar
Physicochemical evaluation of protein folds predicted by threading
A. Kinjo, A. Kidera, Haruki Nakamura, K. Nishikawa
2000European Biophysics Journal14 citations
Semantic Scholar
Nature of Protein Family Signatures: Insights from Singular Value Analysis of Position-Specific Scoring Matrices
A. Kinjo, Haruki Nakamura
2007PLoS ONE13 citations Open access
Semantic Scholar
Composite Structural Motifs of Binding Sites for Delineating Biological Functions of Proteins
A. Kinjo, Haruki Nakamura
2011PLoS ONE12 citations Open access
Semantic Scholar
Cooperative approach for the protein fold recognition
M. Ota, T. Kawabata, A. Kinjo, K. Nishikawa
1999Proteins: Structure, Function, and Bioinformatics12 citations
Semantic Scholar
A new look at an old view of denaturant induced protein unfolding.
Damien Hall, A. Kinjo, Y. Goto
2018Analytical Biochemistry11 citations
Semantic Scholar
Cooperation between phenotypic plasticity and genetic mutations can account for the cumulative selection in evolution
K. Nishikawa, A. Kinjo
2014Biophysics11 citations Open access
Semantic Scholar
The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*
Toshiaki Katayama, K. Arakawa, Mitsuteru Nakao, K. Ono +53 more
2010Journal of Biomedical Semantics10 citations Open access
Semantic Scholar
VaProS: a database-integration approach for protein/genome information retrieval
T. Gojobori, K. Ikeo, Yukie Katayama, T. Kawabata +11 more
2016Journal of Structural and Functional Genomics9 citations Open access
Semantic Scholar
Exhaustive comparison and classification of ligand-binding surfaces in proteins
Yoichi Murakami, K. Kinoshita, A. Kinjo, Haruki Nakamura
2013Protein Science9 citations Open access
Semantic Scholar
Publication of nuclear magnetic resonance experimental data with semantic web technology and the application thereof to biomedical research of proteins
M. Yokochi, N. Kobayashi, E. Ulrich, A. Kinjo +7 more
2016Journal of Biomedical Semantics7 citations Open access
Semantic Scholar
Counterbalance of ligand‐ and self‐coupled motions characterizes multispecificity of ubiquitin
B. Dasgupta, Haruki Nakamura, A. Kinjo
2013Protein Science7 citations Open access
Semantic Scholar
On the optimal contact potential of proteins
A. Kinjo, S. Miyazawa
20077 citations Open access
Semantic Scholar
Predicting Residue-wise Contact Orders of Native Protein Structure from Amino Acid Sequence
A. Kinjo, K. Nishikawa
20057 citations
Semantic Scholar
Comparison of energy components of proteins from thermophilic and mesophilic organisms
A. Kinjo, K. Nishikawa
2001European Biophysics Journal7 citations
Semantic Scholar
A unified statistical model of protein multiple sequence alignment integrating direct coupling and insertions
A. Kinjo
2015Biophysics and Physicobiology6 citations Open access
Semantic Scholar
Rigid‐body motions of interacting proteins dominate multispecific binding of ubiquitin in a shape‐dependent manner
B. Dasgupta, Haruki Nakamura, A. Kinjo
2014Proteins: Structure, Function, and Bioinformatics6 citations Open access
Semantic Scholar
Functional characterization of protein domains common to animal viruses and mouse
A. Kinjo, Y. Kumagai, Huy Q. Dinh, O. Takeuchi +1 more
2011BMC Genomics6 citations Open access
Semantic Scholar
BioHackathon 2015: Semantics of data for life sciences and reproducible research
R. Vos, Toshiaki Katayama, H. Mishima, S. Kawano +73 more
2020F1000Research5 citations Open access
Semantic Scholar
GIRAF: a method for fast search and flexible alignment of ligand binding interfaces in proteins at atomic resolution
A. Kinjo, Haruki Nakamura
2012Biophysics4 citations Open access
Semantic Scholar
Profile conditional random fields for modeling protein families with structural information
A. Kinjo
2009Biophysics4 citations Open access
Semantic Scholar
Monte Carlo simulation of a statistical mechanical model of multiple protein sequence alignment
A. Kinjo
2017Biophysics and Physicobiology3 citations Open access
Semantic Scholar
Essential role of long non-coding RNAs in de novo chromatin modifications: the genomic address code hypothesis
K. Nishikawa, A. Kinjo
2017Biophysical Reviews2 citations Open access
Semantic Scholar
Liquid-theory analogy of direct-coupling analysis of multiple-sequence alignment and its implications for protein structure prediction
A. Kinjo
2015Biophysics and Physicobiology2 citations Open access
Semantic Scholar

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