List of works - Kentaro Tomii

A Novel Antiviral Target Structure Involved in the RNA Binding, Dimerization, and Nuclear Export Functions of the Influenza A Virus Nucleoprotein

scientific article

A comparative analysis of ABC transporters in complete microbial genomes

scientific article published on 01 October 1998

A novel Mitosomal β-barrel Outer Membrane Protein in Entamoeba

scientific article

AIG1 affects in vitro and in vivo virulence in clinical isolates of Entamoeba histolytica.

scientific article published on 19 March 2018

Accurate Classification of Biological and non-Biological Interfaces in Protein Crystal Structures using Subtle Covariation Signals

scientific article published on 30 August 2019

Analysis of amino acid indices and mutation matrices for sequence comparison and structure prediction of proteins

scientific article published on 01 January 1996

Application of the MAFFT sequence alignment program to large data-reexamination of the usefulness of chained guide trees

scientific article

CENP-T provides a structural platform for outer kinetochore assembly

scientific article

Class of cyclic ribosomal peptide synthetic genes in filamentous fungi

scientific article published on 15 December 2015

Convergent evolution in structural elements of proteins investigated using cross profile analysis.

scientific article

Crystallographic characterization of the N-terminal domain of PEX1

scientific article published on 20 October 2004

DeepECA: an end-to-end learning framework for protein contact prediction from a multiple sequence alignment

scientific article published on 09 January 2020

Discrimination of Golgi Type II Membrane Proteins Based on Their Hydropathy Profiles and the Amino Acid Propensities of Their Transmembrane Regions

scientific article published on 07 January 2011

Evolutionary analyses of caspase-8 and its paralogs: Deep origins of the apoptotic signaling pathways

scientific article published on 22 May 2015

EzCatDB: the enzyme reaction database, 2015 update.

scientific article

FORTE: a profile-profile comparison tool for protein fold recognition.

scientific article published on 5 February 2004

Fine-tuning of protein domain boundary by minimizing potential coiled coil regions

scientific article published on 16 December 2006

Functional conservation of the apoptotic machinery from coral to man: the diverse and complex Bcl-2 and caspase repertoires of Acropora millepora.

scientific article published on 16 January 2016

Genome-Wide Analysis of Known and Potential Tetraspanins in Entamoeba histolytica

scientific article published on 03 November 2019

HMGB1 signaling phosphorylates Ku70 and impairs DNA damage repair in Alzheimer's disease pathology

scientific article published on 11 October 2021

Identification of cargo proteins specific for the nucleocytoplasmic transport carrier transportin by combination of an in vitro transport system and stable isotope labeling by amino acids in cell culture (SILAC)-based quantitative proteomics.

scientific article published on 19 October 2012

Identification of hepta-histidine as a candidate drug for Huntington's disease by in silico-in vitro- in vivo-integrated screens of chemical libraries

scientific article

Identification of new abscisic acid receptor agonists using a wheat cell-free based drug screening system.

scientific article published on 9 March 2018

Import of Entamoeba histolytica Mitosomal ATP Sulfurylase Relies on Internal Targeting Sequences

scientific article published on 12 August 2020

Mammalian NUMT insertion is non-random ⬇️

scientific article published on July 3, 2012

MitoFates: improved prediction of mitochondrial targeting sequences and their cleavage sites.

scientific article

Molecular architecture of the active mitochondrial protein gate

scientific article

Novel mechanism of interaction of p85 subunit of phosphatidylinositol 3-kinase and ErbB3 receptor-derived phosphotyrosyl peptides.

scientific article

Origin and Evolutionary Alteration of the Mitochondrial Import System in Eukaryotic Lineages

scientific article

PDB‐scale analysis of known and putative ligand‐binding sites with structural sketches ⬇️

scientific article published on November 24, 2011

PoSSuM v.2.0: data update and a new function for investigating ligand analogs and target proteins of small-molecule drugs.

scientific article

PoSSuM: a database of similar protein-ligand binding and putative pockets ⬇️

scientific article published on December 1, 2011

Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment

scientific article

Protein ligand-binding site comparison by a reduced vector representation derived from multidimensional scaling of generalized description of binding sites.

scientific article

Protein sequence-similarity search acceleration using a heuristic algorithm with a sensitive matrix

scientific article

Protein structure prediction using a variety of profile libraries and 3D verification.

scientific article

Revisiting amino acid substitution matrices for identifying distantly related proteins.

scientific article

SAHG, a comprehensive database of predicted structures of all human proteins ⬇️

scientific article published on November 3, 2010

ScreenCap3: Improving prediction of caspase-3 cleavage sites using experimentally verified noncleavage sites.

scientific article

Simple adjustment of the sequence weight algorithm remarkably enhances PSI-BLAST performance.

scientific article

Structure of the N-terminal domain of PEX1 AAA-ATPase. Characterization of a putative adaptor-binding domain

scientific article published in Journal of Biological Chemistry

Systematic Exploration of an Efficient Amino Acid Substitution Matrix: MIQS.

scientific article

Template-based quaternary structure prediction of proteins using enhanced profile-profile alignments.

scientific article published on 27 November 2017

The apoptotic initiator caspase-8: its functional ubiquity and genetic diversity during animal evolution.

scientific article published on 8 September 2014

Tyrosine phosphorylation of the GARU E3 ubiquitin ligase promotes gibberellin signalling by preventing GID1 degradation.

scientific article published on 17 October 2017

Visualization of conformational distribution of short to medium size segments in globular proteins and identification of local structural motifs.

scientific article

List of works by Kentaro Tomii

A Novel Antiviral Target Structure Involved in the RNA Binding, Dimerization, and Nuclear Export Functions of the Influenza A Virus Nucleoprotein

A comparative analysis of ABC transporters in complete microbial genomes

A novel Mitosomal β-barrel Outer Membrane Protein in Entamoeba

AIG1 affects in vitro and in vivo virulence in clinical isolates of Entamoeba histolytica.

Accurate Classification of Biological and non-Biological Interfaces in Protein Crystal Structures using Subtle Covariation Signals

Analysis of amino acid indices and mutation matrices for sequence comparison and structure prediction of proteins

Application of the MAFFT sequence alignment program to large data-reexamination of the usefulness of chained guide trees

CENP-T provides a structural platform for outer kinetochore assembly

Class of cyclic ribosomal peptide synthetic genes in filamentous fungi

Convergent evolution in structural elements of proteins investigated using cross profile analysis.

Crystallographic characterization of the N-terminal domain of PEX1

DeepECA: an end-to-end learning framework for protein contact prediction from a multiple sequence alignment

Discrimination of Golgi Type II Membrane Proteins Based on Their Hydropathy Profiles and the Amino Acid Propensities of Their Transmembrane Regions

Evolutionary analyses of caspase-8 and its paralogs: Deep origins of the apoptotic signaling pathways

EzCatDB: the enzyme reaction database, 2015 update.

FORTE: a profile-profile comparison tool for protein fold recognition.

Fine-tuning of protein domain boundary by minimizing potential coiled coil regions

Functional conservation of the apoptotic machinery from coral to man: the diverse and complex Bcl-2 and caspase repertoires of Acropora millepora.

Genome-Wide Analysis of Known and Potential Tetraspanins in Entamoeba histolytica

HMGB1 signaling phosphorylates Ku70 and impairs DNA damage repair in Alzheimer's disease pathology

Identification of cargo proteins specific for the nucleocytoplasmic transport carrier transportin by combination of an in vitro transport system and stable isotope labeling by amino acids in cell culture (SILAC)-based quantitative proteomics.

Identification of hepta-histidine as a candidate drug for Huntington's disease by in silico-in vitro- in vivo-integrated screens of chemical libraries

Identification of new abscisic acid receptor agonists using a wheat cell-free based drug screening system.

Import of Entamoeba histolytica Mitosomal ATP Sulfurylase Relies on Internal Targeting Sequences

Mammalian NUMT insertion is non-random ⬇️

MitoFates: improved prediction of mitochondrial targeting sequences and their cleavage sites.

Molecular architecture of the active mitochondrial protein gate

Novel mechanism of interaction of p85 subunit of phosphatidylinositol 3-kinase and ErbB3 receptor-derived phosphotyrosyl peptides.

Origin and Evolutionary Alteration of the Mitochondrial Import System in Eukaryotic Lineages

PDB‐scale analysis of known and putative ligand‐binding sites with structural sketches ⬇️

PoSSuM v.2.0: data update and a new function for investigating ligand analogs and target proteins of small-molecule drugs.

PoSSuM: a database of similar protein-ligand binding and putative pockets ⬇️

Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment

Protein ligand-binding site comparison by a reduced vector representation derived from multidimensional scaling of generalized description of binding sites.

Protein sequence-similarity search acceleration using a heuristic algorithm with a sensitive matrix

Protein structure prediction using a variety of profile libraries and 3D verification.

Revisiting amino acid substitution matrices for identifying distantly related proteins.

SAHG, a comprehensive database of predicted structures of all human proteins ⬇️

ScreenCap3: Improving prediction of caspase-3 cleavage sites using experimentally verified noncleavage sites.

Simple adjustment of the sequence weight algorithm remarkably enhances PSI-BLAST performance.

Structure of the N-terminal domain of PEX1 AAA-ATPase. Characterization of a putative adaptor-binding domain

Systematic Exploration of an Efficient Amino Acid Substitution Matrix: MIQS.

Template-based quaternary structure prediction of proteins using enhanced profile-profile alignments.

The apoptotic initiator caspase-8: its functional ubiquity and genetic diversity during animal evolution.

Tyrosine phosphorylation of the GARU E3 ubiquitin ligase promotes gibberellin signalling by preventing GID1 degradation.

Visualization of conformational distribution of short to medium size segments in globular proteins and identification of local structural motifs.