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

von Kinjo, Akira R.
Veröffentlicht in Biophys Physicobiol (2015)

Profile conditional random fields for modeling protein families with structural information

von Kinjo, Akira R.
Veröffentlicht in Biophysics (Nagoya-shi) (2009)

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

von Kinjo, Akira R.
Veröffentlicht in Biophys Physicobiol (2016)

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

von Kinjo, Akira R.
Veröffentlicht in Biophys Physicobiol (2017)

Competition between Protein Folding and Aggregation with Molecular Chaperones in Crowded Solutions: Insight from Mesoscopic Simulations

von Kinjo, Akira R., Takada, Shoji
Veröffentlicht 2003

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

von Kinjo, Akira R, Nishikawa, Ken
Veröffentlicht 2006

Nature of Protein Family Signatures: Insights from Singular Value Analysis of Position-Specific Scoring Matrices

von Kinjo, Akira R., Nakamura, Haruki
Veröffentlicht 2008

Composite Structural Motifs of Binding Sites for Delineating Biological Functions of Proteins

von Kinjo, Akira R., Nakamura, Haruki
Veröffentlicht 2012

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

von Kinjo, Akira R., Nakamura, Haruki
Veröffentlicht in Biophysics (Nagoya-shi) (2012)

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

von Nishikawa, Ken, Kinjo, Akira R.
Veröffentlicht in Biophysics (Nagoya-shi) (2014)

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

von Kinjo, Akira R., Nakamura, Haruki
Veröffentlicht in Biophysics (Nagoya-shi) (2007)

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

von Kinjo, Akira R., Nishikawa, Ken
Veröffentlicht in Biophysics (Nagoya-shi) (2005)

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

von Nishikawa, Ken, Kinjo, Akira R.
Veröffentlicht in Biophys Rev (2017)

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

von Nishikawa, Ken, Kinjo, Akira R.
Veröffentlicht in Biophys Rev (2018)

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

von Kinjo, Akira R., Yamashita, Reiko, Nakamura, Haruki
Veröffentlicht 2010

Counterbalance of ligand- and self-coupled motions characterizes multispecificity of Ubiquitin

von Dasgupta, Bhaskar, Nakamura, Haruki, Kinjo, Akira R
Veröffentlicht 2013

Molmil: a molecular viewer for the PDB and beyond

von Bekker, Gert-Jan, Nakamura, Haruki, Kinjo, Akira R.
Veröffentlicht in J Cheminform (2016)

Exhaustive comparison and classification of ligand-binding surfaces in proteins

von Murakami, Yoichi, Kinoshita, Kengo, Kinjo, Akira R, Nakamura, Haruki
Veröffentlicht 2013

Specific Non-Local Interactions Are Not Necessary for Recovering Native Protein Dynamics

von Dasgupta, Bhaskar, Kasahara, Kota, Kamiya, Narutoshi, Nakamura, Haruki, Kinjo, Akira R.
Veröffentlicht 2014

SeSAW: balancing sequence and structural information in protein functional mapping

von Standley, Daron M., Yamashita, Reiko, Kinjo, Akira R., Toh, Hiroyuki, Nakamura, Haruki
Veröffentlicht 2010