Kentaro Tomii

发表

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

Daisuke Kihara, Keehyoung Joo, Daisuke Kuroda, 2016, Proteins.

Template‐based quaternary structure prediction of proteins using enhanced profile–profile alignments

Toshiyuki Oda, Tsukasa Nakamura, Kentaro Tomii, 2017, Proteins.

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

Toshiyuki Oda, Kentaro Tomii, Kyungtaek Lim, 2017, BMC Bioinformatics.

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

Yasuo Tabei, Kana Shimizu, Koji Tsuda, 2011, Nucleic Acids Res..

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

Toshiyuki Oda, Kentaro Tomii, Kyungtaek Lim, 2016, bioRxiv.

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

Yutaka Akiyama, Kentaro Tomii, Y. Akiyama, 2004, Bioinform..

EzCatDB: the enzyme reaction database, 2015 update

Tsuyoshi Kato, Nozomi Nagano, Kentaro Tomii, 2014, Nucleic Acids Res..

Protein Properties

Kentaro Tomii, 2019, Encyclopedia of Bioinformatics and Computational Biology.

Compound‐protein interaction prediction with end‐to‐end learning of neural networks for graphs and sequences

Jun Sese, Masashi Tsubaki, Kentaro Tomii, 2018, Bioinform..

Neural networks for protein structure and function prediction and dynamic analysis

Kentaro Tomii, Yuko Tsuchiya, K. Tomii, 2020, Biophysical Reviews.

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

Takatsugu Hirokawa, Chie Motono, Kentaro Tomii, 2005, Proteins.

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

Kazutaka Katoh, Kazunori D. Yamada, Kentaro Tomii, 2016, Bioinform..

Predicting mostly disordered proteins by using structure-unknown protein data

Yoichi Muraoka, Shuichi Hirose, Kana Shimizu, 2007, BMC Bioinform..

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

Kengo Kinoshita, Kana Shimizu, Tamotsu Noguchi, 2010, Nucleic Acids Res..

Deep Neural Network for Protein Contact Prediction by Weighting Sequences in a Multiple Sequence Alignment

Hiroyuki Fukuda, Kentaro Tomii, K. Tomii, 2018, bioRxiv.

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

Yasuo Tabei, Kana Shimizu, Koji Tsuda, 2012, Proteins.

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

Kentaro Tomii, Hiroyuki Fukuda, K. Tomii, 2020, BMC Bioinformatics.

Parallelization of MAFFT for large-scale multiple sequence alignments

Kazutaka Katoh, Kazunori D. Yamada, Kentaro Tomii, 2018, Bioinform..

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

Kenji Mizuguchi, Kazunori D. Yamada, Kentaro Tomii, 2014, Nucleic Acids Res..

Revisiting amino acid substitution matrices for identifying distantly related proteins

Kazunori D. Yamada, Kentaro Tomii, Kazunori D. Yamada, 2013, Bioinform..

2P-009 Identification of essential structural variables for medium-size protein-segment and application to structural class assignment(The 46th Annual Meeting of the Biophysical Society of Japan)

Junichi Higo, Kentaro Tomii, Kazuyoshi Ikeda, 2008 .

Maximum Likelihood Superposition of Protein Structures

Tsuyoshi Kato, Kiyoshi Asai, Koji Tsuda, 2003 .

Meta-Align: A Novel HMM-based Algorithm for Pairwise Alignment of Error-Prone Sequencing Reads

Steven E. Brenner, Degui Zhi, Kentaro Tomii, 2020 .

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

Shinya Honda, Yoshito Sawada, Kentaro Tomii, 2012, BMC Bioinformatics.

Systematic Detection of Protein Structural Motifs

Minoru Kanehisa, Kentaro Tomii, M. Kanehisa, 1999, Pattern Discovery in Biomolecular Data.

A New Variational Framework for Rigid-Body Alignment

Tsuyoshi Kato, Kiyoshi Asai, Koji Tsuda, 2004, SSPR/SPR.

An Ensemble Reweighting Method for Combining the Information of Experiments and Simulations

Kentaro Tomii, Yu Yamamori, 2021 .

Fellowships, Grants, & Awards

Yoichi Muraoka, Shuichi Hirose, Kana Shimizu, 2005, Environmental Health Perspectives.

Effects of the difference in similarity measures on the comparison of ligand-binding pockets using a reduced vector representation of pockets

Kentaro Tomii, K. Tomii, Tsukasa Nakamura, 2016, Biophysics and physicobiology.

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

Kenichiro Imai, Kentaro Tomii, Szu-Chin Fu, 2014, Proteomics.

Structure of the N-terminal Domain of PEX1 AAA-ATPase

Yutaka Akiyama, Hidekazu Hiroaki, Kentaro Tomii, 2004, Journal of Biological Chemistry.

Molecular architecture of the active mitochondrial protein gate

Arne Elofsson, Paul Horton, Kenichiro Imai, 2015, Science.

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

Yutaka Akiyama, Hidekazu Hiroaki, Kentaro Tomii, 2005, The Journal of biological chemistry.

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

Kentaro Tomii, K. Tomii, Tsukasa Nakamura, 2016, Methods.

Novel Mechanism of Interaction of p85 Subunit of Phosphatidylinositol 3-Kinase and ErbB3 Receptor-derived Phosphotyrosyl Peptides*

Akihiko Konagaya, Makoto Taiji, Tetsu Narumi, 2005, Journal of Biological Chemistry.

A New Variational Framework for Rigid -

Kiyoshi Asai, Koji Tsuda, Kentaro Tomii, 2004 .

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

Kentaro Tomii, Kazunori Yamada, 2016, Methods in molecular biology.

AAindex: A Database of Amino Acid Indices and Mutation Matrices

Minoru Kanehisa, Kentaro Tomii, M. Kanehisa, 1995 .