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

por Kinjo, Akira R.
Publicado no Biophys Physicobiol (2015)

Profile conditional random fields for modeling protein families with structural information

por Kinjo, Akira R.
Publicado no Biophysics (Nagoya-shi) (2009)

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

por Kinjo, Akira R.
Publicado no Biophys Physicobiol (2016)

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

por Kinjo, Akira R.
Publicado no Biophys Physicobiol (2017)

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

por Kinjo, Akira R., Takada, Shoji
Publicado em 2003

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

por Kinjo, Akira R, Nishikawa, Ken
Publicado em 2006

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

por Kinjo, Akira R., Nakamura, Haruki
Publicado em 2008

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

por Kinjo, Akira R., Nakamura, Haruki
Publicado em 2012

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

por Kinjo, Akira R., Nakamura, Haruki
Publicado no Biophysics (Nagoya-shi) (2012)

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

por Nishikawa, Ken, Kinjo, Akira R.
Publicado no Biophysics (Nagoya-shi) (2014)

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

por Kinjo, Akira R., Nakamura, Haruki
Publicado no 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

por Kinjo, Akira R., Nishikawa, Ken
Publicado no Biophysics (Nagoya-shi) (2005)

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

por Nishikawa, Ken, Kinjo, Akira R.
Publicado no Biophys Rev (2017)

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

por Nishikawa, Ken, Kinjo, Akira R.
Publicado no Biophys Rev (2018)

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

por Kinjo, Akira R., Yamashita, Reiko, Nakamura, Haruki
Publicado em 2010

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

por Dasgupta, Bhaskar, Nakamura, Haruki, Kinjo, Akira R
Publicado em 2013

Molmil: a molecular viewer for the PDB and beyond

por Bekker, Gert-Jan, Nakamura, Haruki, Kinjo, Akira R.
Publicado no J Cheminform (2016)

Exhaustive comparison and classification of ligand-binding surfaces in proteins

por Murakami, Yoichi, Kinoshita, Kengo, Kinjo, Akira R, Nakamura, Haruki
Publicado em 2013

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

por Dasgupta, Bhaskar, Kasahara, Kota, Kamiya, Narutoshi, Nakamura, Haruki, Kinjo, Akira R.
Publicado em 2014

SeSAW: balancing sequence and structural information in protein functional mapping

por Standley, Daron M., Yamashita, Reiko, Kinjo, Akira R., Toh, Hiroyuki, Nakamura, Haruki
Publicado em 2010