Kentaro Tomii

Publication Activity (10 Years)

Years Active: 2004-2023
Publications (10 Years): 6

Top Topics

Multiple Sequence Alignments

Finding Similar

Physicochemical Properties

Update Operations

Top Venues

Nucleic Acids Res.

J. Chem. Inf. Model.

Publications

Yuko Tsuchiya, Tomoki Yonezawa, Yu Yamamori, Hiroko Inoura, Masanori Osawa, Kazuyoshi Ikeda, Kentaro Tomii
PoSSuM v.3: A Major Expansion of the PoSSuM Database for Finding Similar Binding Sites of Proteins. J. Chem. Inf. Model. 63 (23) (2023)
Hiroyuki Fukuda, Kentaro Tomii
DeepECA: an end-to-end learning framework for protein contact prediction from a multiple sequence alignment. BMC Bioinform. 21 (1) (2020)
Masashi Tsubaki, Kentaro Tomii, Jun Sese
Compound-protein interaction prediction with end-to-end learning of neural networks for graphs and sequences. Bioinform. 35 (2) (2019)
Tsukasa Nakamura, Kazunori D. Yamada, Kentaro Tomii, Kazutaka Katoh
Parallelization of MAFFT for large-scale multiple sequence alignments. Bioinform. 34 (14) (2018)
Toshiyuki Oda, Kyungtaek Lim, Kentaro Tomii
Simple adjustment of the sequence weight algorithm remarkably enhances PSI-BLAST performance. BMC Bioinform. 18 (1) (2017)
Kazunori D. Yamada, Kentaro Tomii, Kazutaka Katoh
Application of the MAFFT sequence alignment program to large data - reexamination of the usefulness of chained guide trees. Bioinform. 32 (21) (2016)
Jun-Ichi Ito, Kazuyoshi Ikeda, Kazunori D. Yamada, Kenji Mizuguchi, Kentaro Tomii
PoSSuM v.2.0: data update and a new function for investigating ligand analogs and target proteins of small-molecule drugs. Nucleic Acids Res. 43 (Database-Issue) (2015)
Nozomi Nagano, Naoko Nakayama, Kazuyoshi Ikeda, Masaru Fukuie, Kiyonobu Yokota, Takuo Doi, Tsuyoshi Kato, Kentaro Tomii
EzCatDB: the enzyme reaction database, 2015 update. Nucleic Acids Res. 43 (Database-Issue) (2015)
Kazunori D. Yamada, Kentaro Tomii
Revisiting amino acid substitution matrices for identifying distantly related proteins. Bioinform. 30 (3) (2014)
Kentaro Tomii, Yoshito Sawada, Shinya Honda
Convergent evolution in structural elements of proteins investigated using cross profile analysis. BMC Bioinform. 13 (2012)
Jun-Ichi Ito, Yasuo Tabei, Kana Shimizu, Koji Tsuda, Kentaro Tomii
PoSSuM: a database of similar protein-ligand binding and putative pockets. Nucleic Acids Res. 40 (Database-Issue) (2012)
Chie Motono, Junichi Nakata, Ryotaro Koike, Kana Shimizu, Matsuyuki Shirota, Takayuki Amemiya, Kentaro Tomii, Nozomi Nagano, Naofumi Sakaya, Kiyotaka Misoo, Miwa Sato, Akinori Kidera, Hidekazu Hiroaki, Tsuyoshi Shirai, Kengo Kinoshita, Tamotsu Noguchi, Motonori Ota
SAHG, a comprehensive database of predicted structures of all human proteins. Nucleic Acids Res. 39 (Database-Issue) (2011)
Kana Shimizu, Yoichi Muraoka, Shuichi Hirose, Kentaro Tomii, Tamotsu Noguchi
Predicting mostly disordered proteins by using structure-unknown protein data. BMC Bioinform. 8 (2007)
Kentaro Tomii, Yutaka Akiyama
FORTE: a profile-profile comparison tool for protein fold recognition. Bioinform. 20 (4) (2004)
Tsuyoshi Kato, Koji Tsuda, Kentaro Tomii, Kiyoshi Asai
A New Variational Framework for Rigid-Body Alignment. SSPR/SPR (2004)