Helix encoder: a compound-protein interaction prediction model specifically designed for class A GPCRs Reviewed International journal

Haruki Yamane, Takashi Ishida

Frontiers in Bioinformatics   2023.5

Protein Model Quality Estimation Using Molecular Dynamics Simulation Reviewed International journal

Jason Kurniawan, Takashi Ishida

ACS Omega   2022.7

How to select the best model from AlphaFold2 structures?

Yuma Takei, Takashi Ishida

2022.4

A Benchmark Dataset for Evaluating Practical Performance of Model Quality Assessment of Homology Models Reviewed International journal

Yuma Takei, Takashi Ishida

Bioengineering   9 ( 3 )   118 - 118   2022.3

Modeling SARS‐CoV‐2 proteins in the CASP‐commons experiment Reviewed International coauthorship International journal

Andriy Kryshtafovych, John Moult, Wendy M. Billings, Dennis Della Corte, Krzysztof Fidelis, Sohee Kwon, Kliment Olechnovič, Chaok Seok, Česlovas Venclovas, Jonghun Won, CASP‐COVID participants

Proteins: Structure, Function, and Bioinformatics   2021.12

Computer aided drug discovery review for infectious diseases with case study of anti-Chagas project Reviewed International journal

Nobuaki Yasuo, Takashi Ishida, Masakazu Sekijima

Parasitology International   2021.8

Taxonomic and Gene Category Analyses of Subgingival Plaques from a Group of Japanese Individuals with and without Periodontitis Reviewed International journal

Kazuki Izawa, Kazuko Okamoto-Shibayama, Daichi Kita, Sachiyo Tomita, Atsushi Saito, Takashi Ishida, Masahito Ohue, Yutaka Akiyama, Kazuyuki Ishihara

International Journal of Molecular Sciences   22 ( 10 )   5298 - 5298   2021.5

End-to-end learning for compound activity prediction based on binding pocket information Reviewed International coauthorship International journal

Toshitaka Tanebe, Takashi Ishida

BMC Bioinformatics   2021.5

P3CMQA: Single-Model Quality Assessment Using 3DCNN with Profile-Based Features Reviewed International journal

Yuma Takei, Takashi Ishida

Bioengineering   8 ( 3 )   40 - 40   2021.3

Single-Step Retrosynthesis Prediction Based on the Identification of Potential Disconnection Sites Using Molecular Substructure Fingerprints Reviewed International journal

Haris Hasic, Takashi Ishida

Journal of Chemical Information and Modeling   61 ( 2 )   641 - 652   2021.2

Mathematical proof of the third order accuracy of the speedy double bootstrap method Reviewed International coauthorship International journal

Aizhen Ren, Takashi Ishida, Yutaka Akiyama

Communications in Statistics - Theory and Methods   2020.8

Development of Computational Pipeline Software for Genome/Exome Analysis on the K Computer

Takashi Ishida

Supercomputing Frontiers and Innovations   2020.3

Sequence alignment using machine learning for accurate template-based protein structure prediction Reviewed International journal

Shuichiro Makigaki, Takashi Ishida

Bioinformatics   2020.1

Sequence alignment generation using intermediate sequence search for homology modeling Reviewed International journal

Shuichiro Makigaki, Takashi Ishida

Computational and Structural Biotechnology Journal   2020

A prospective compound screening contest identified broader inhibitors for Sirtuin 1. Reviewed

Chiba S, Ohue M, Gryniukova A, Borysko P, Zozulya S, Yasuo N, Yoshino R, Ikeda K, Shin WH, Kihara D, Iwadate M, Umeyama H, Ichikawa T, Teramoto R, Hsin KY, Gupta V, Kitano H, Sakamoto M, Higuchi A, Miura N, Yura K, Mochizuki M, Ramakrishnan C, Thangakani AM, Velmurugan D, Gromiha MM, Nakane I, Uchida N, Hakariya H, Tan M, Nakamura HK, Suzuki SD, Ito T, Kawatani M, Kudoh K, Takashina S, Yamamoto KZ, Moriwaki Y, Oda K, Kobayashi D, Okuno T, Minami S, Chikenji G, Prathipati P, Nagao C, Mohsen A, Ito M, Mizuguchi K, Honma T, Ishida T, Hirokawa T, Akiyama Y, Sekijima M

Scientific reports   9 ( 1 )   19585   2019.12

Protein model accuracy estimation based on local structure quality assessment using 3D convolutional neural network Reviewed International journal

Rin Sato, Takashi Ishida

PLOS ONE   14 ( 9 )   2019.9

An iterative compound screening contest method for identifying target protein inhibitors using the tyrosine-protein kinase Yes Reviewed

Shuntaro Chiba, Takashi Ishida, Kazuyoshi Ikeda, Masahiro Mochizuki, Reiji Teramoto, Y-h. Taguchi, Mitsuo Iwadate, Hideaki Umeyama, Chandrasekaran Ramakrishnan, A. Mary Thangakani, D. Velmurugan, M. Michael Gromiha, Tatsuya Okuno, Koya Kato, Shintaro Minami, George Chikenji, Shogo D. Suzuki, Keisuke Yanagisawa, Woong-Hee Shin, Daisuke Kihara, Kazuki Z. Yamamoto, Yoshitaka Moriwaki, Nobuaki Yasuo, Ryunosuke Yoshino, Sergey Zozulya, Petro Borysko, Roman Stavniichuk, Teruki Honma, Takatsugu Hirokawa, Yutaka Akiyama, Masakazu Sekijima

SCIENTIFIC REPORTS   7 ( 12038 )   1 - 13   2017.9

In silico, in vitro, X-ray crystallography, and integrated strategies for discovering spermidine synthase inhibitors for Chagas disease Reviewed

Ryunosuke Yoshino, Nobuaki Yasuo, Yohsuke Hagiwara, Takashi Ishida, Daniel Ken Inaoka, Yasushi Amano, Yukihiro Tateishi, Kazuki Ohno, Ichiji Namatame, Tatsuya Niimi, Masaya Orita, Kiyoshi Kita, Yutaka Akiyama, Masakazu Sekijima

SCIENTIFIC REPORTS   7 ( 1 )   6666   2017.7

Spresso: an ultrafast compound pre-screening method based on compound decomposition

Keisuke Yanagisawa, Shunta Komine, Shogo D Suzuki, Masahito Ohue, Takashi Ishida, Yutaka Akiyama

Bioinformatics   33 ( 23 )   3836 - 3843   2017.3

GPU-acceleration of sequence homology searches with database subsequence clustering

S Suzuki, M Kakuta, T Ishida, Y Akiyama

PLoS one   2016

Identification of potential inhibitors based on compound proposal contest: Tyrosine-protein kinase Yes as a target. Reviewed

Chiba S, Ikeda K, Ishida T, Gromiha MM, Taguchi YH, Iwadate M, Umeyama H, Hsin KY, Kitano H, Yamamoto K, Sugaya N, Kato K, Okuno T, Chikenji G, Mochizuki M, Yasuo N, Yoshino R, Yanagisawa K, Ban T, Teramoto R, Ramakrishnan C, Thangakani AM, Velmurugan D, Prathipati P, Ito J, Tsuchiya Y, Mizuguchi K, Honma T, Hirokawa T, Akiyama Y, Sekijima M

Scientific reports   5   17209   2015.11

Protein-protein docking on hardware accelerators: comparison of GPU and MIC architectures

Shimoda, Takehiro, Suzuki, Shuji, Ohue, Masahito, Ishida, Takashi, Akiyama, Yutaka

Bmc Systems Biology   9   2015

Faster sequence homology searches by clustering subsequences

Suzuki, Shuji, Kakuta, Masanori, Ishida, Takashi, Akiyama, Yutaka

Bioinformatics   31 ( 8 )   2015

Drug Clearance Pathway Prediction Based on Semi-supervised Learning

Yanagisawa, Keisuke, Ishida, Takashi, Akiyama, Yutaka

IPSJ Transactions on Bioinformatics   8   21 - 27   2015

MEGADOCK 4.0: an ultra-high-performance protein-protein docking software for heterogeneous supercomputers

Ohue, Masahito, Shimoda, Takehiro, Suzuki, Shuji, Matsuzaki, Yuri, Ishida, Takashi, Akiyama, Yutaka

Bioinformatics   30 ( 22 )   2014

GHOSTX: An Improved Sequence Homology Search Algorithm Using a Query Suffix Array and a Database Suffix Array

Suzuki, Shuji, Kakuta, Masanori, Ishida, Takashi, Akiyama, Yutaka

Plos One   9 ( 8 )   2014

MEGADOCK: An All-to-All Protein-Protein Interaction Prediction System Using Tertiary Structure Data

Ohue, Masahito, Matsuzaki, Yuri, Uchikoga, Nobuyuki, Ishida, Takashi, Akiyama, Yutaka

Protein and Peptide Letters   21 ( 8 )   2014

(DP2)-P-2: database of disordered protein predictions

Oates, Matt E., Romero, Pedro, Ishida, Takashi, Ghalwash, Mohamed, Mizianty, Marcin J., Xue, Bin, Dosztanyi, Zsuzsanna, Uversky, Vladimir N., Obradovic, Zoran, Kurgan, Lukasz, Dunker, A. Keith, Gough, Julian

Nucleic Acids Research   41 ( D1 )   2013

Assessing statistical reliability of phylogenetic trees via a speedy double bootstrap method

Ren, Aizhen, Ishida, Takashi, Akiyama, Yutaka

Molecular Phylogenetics and Evolution   67 ( 2 )   2013

Acceleration of sequence clustering using longest common subsequence filtering

Namiki, Youhei, Ishida, Takashi, Akiyama, Yutaka

Bmc Bioinformatics   14   2013

Improvement of Protein-Protein Interaction Prediction by Integrating Template-Based and Template-Free Protein Docking.

Masahito Ohue, Yuri Matsuzaki, Takehiro Shimoda, Takashi Ishida 0002, Yutaka Akiyama

ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics. ACM-BCB 2013(BCB)   666 - 666   2013

An ultra-fast computing pipeline for metagenome analysis with next-generation DNA sequencers

Suzuki, Shuji, Ishida, Takashi, Akiyama, Yutaka, IEEE

2012 Sc Companion: High Performance Computing, Networking, Storage and Analysis (Scc)   2012

Improvement of the Protein-Protein Docking Prediction by Introducing a Simple Hydrophobic Interaction Model: An Application to Interaction Pathway Analysis.

Masahito Ohue, Yuri Matsuzaki, Takashi Ishida 0002, Yutaka Akiyama

Pattern Recognition in Bioinformatics - 7th IAPR International Conference(PRIB)   178 - 187   2012

Fast DNA Sequence Clustering Based on Longest Common Subsequence.

Youhei Namiki, Takashi Ishida 0002, Yutaka Akiyama

Emerging Intelligent Computing Technology and Applications - 8th International Conference   453 - 460   2012

Absolute quality evaluation of protein model structures using statistical potentials with respect to the native and reference states

Shirota, Matsuyuki, Ishida, Takashi, Kinoshita, Kengo

Proteins-Structure Function and Bioinformatics   79 ( 5 )   2011

Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology

Fleishman, Sarel J., Whitehead, Timothy A., Strauch, Eva-Maria, Corn, Jacob E., Qin, Sanbo, Zhou, Huan-Xiang, Mitchell, Julie C., Demerdash, Omar N. A., Takeda-Shitaka, Mayuko, Terashi, Genki, Moal, Iain H., Li, Xiaofan, Bates, Paul A., Zacharias, Martin, Park, Hahnbeom, Ko, Jun-su, Lee, Hasup, Seok, Chaok, Bourquard, Thomas, Bernauer, Julie, Poupon, Anne, Aze, Jerome, Soner, Seren, Ovali, Sefik Kerem, Ozbek, Pemra, Ben Tal, Nir, Haliloglu, Turkan, Hwang, Howook, Vreven, Thom, Pierce, Brian G., Weng, Zhiping, Perez-Cano, Laura, Pons, Caries, Fernandez-Recio, Juan, Jiang, Fan, Yang, Feng, Gong, Xinqi, Cao, Libin, Xu, Xianjin, Liu, Bin, Wang, Panwen, Li, Chunhua, Wang, Cunxin, Rober, Charles H., Guharoy, Mainak, Liu, Shiyong, Huang, Yangyu, Li, Lin, Guo, Dachuan, Chen, Ying, Xiao, Yi, London, Nir, Itzhaki, Zohar, Schueler-Furman, Ora, Inbar, Yuval, Potapov, Vladimir, Cohen, Mati, Schreiber, Gideon, Tsuchiya, Yuko, Kanamori, Eiji, Standley, Daron M., Nakamura, Haruki, Kinoshita, Kengo, Driggers, Camden M., Hall, Robert G., Morgan, Jessica L., Hsu, Victor L., Zhan, Jian, Yang, Yuedong, Zhou, Yaoqi, Kastritis, Panagiotis L., Bonvin, Alexandre M. J. J., Zhang, Weiyi, Camacho, Carlos J., Kilambi, Krishna P., Sircar, Aroop, Gray, Jeffrey J., Ohue, Masahito, Uchikoga, Nobuyuki, Matsuzaki, Yuri, Ishida, Takashi, Akiyama, Yutaka, Khashan, Raed, Bush, Stephen, Fouches, Denis, Tropsha, Alexander, Esquivel-Rodriguez, Juan, Kihara, Daisuke, Stranges, P. Benjamin, Jacak, Ron, Kuhlman, Brian, Huang, Sheng-You, Zou, Xiaoqin, Wodak, Shoshana J., Janin, Joel, Baker, David

Journal of Molecular Biology   414 ( 2 )   2011

Analyses on hydrophobicity and attractiveness of all-atom distance-dependent potentials

Shirota, Matsuyuki, Ishida, Takashi, Kinoshita, Kengo

Protein Science   18 ( 9 )   2009

PiSite: a database of protein interaction sites using multiple binding states in the PDB

Higurashi, Miho, Ishida, Takashi, Kinoshita, Kengo

Nucleic Acids Research   37   2009

Identification of transient hub proteins and the possible structural basis for their multiple interactions

Higurashi, Miho, Ishida, Takashi, Kinoshita, Kengo

Protein Science   17 ( 1 )   2008

Prediction of disordered regions in proteins based on the meta approach

Ishida, Takashi, Kinoshita, Kengo

Bioinformatics   24 ( 11 )   2008

PrDOS: prediction of disordered protein regions from amino acid sequence

Ishida, Takashi, Kinoshita, Kengo

Nucleic Acids Research   35   2007

Potential for assessing quality of protein structure based on contact number prediction

Ishida, Takashi, Nakamura, Shugo, Shimizu, Kentaro

Proteins-Structure Function and Bioinformatics   64 ( 4 )   2006

Aggregation mechanism of polyglutamine diseases revealed using quantum chemical calculations, fragment molecular orbital calculations, molecular dynamics simulations, and binding free energy calculations

Tsukamoto, Koki, Shimizu, Hideaki, Ishida, Takashi, Akiyama, Yutaka, Nukina, Nobuyuki

Journal of Molecular Structure-Theochem   778 ( 1-3 )   2006

Development of an ab initio protein structure prediction system ABLE.

Ishida, Takashi, Nishimura, Takeshi, Nozaki, Makoto, Inoue, Tsuyoshi, Terada, Tohru, Nakamura, Shugo, Shimizu, Kentaro

Genome informatics. International Conference on Genome Informatics   14   2003

Current Status of in Silico Drug Discovery for Neglected Tropical Diseases

ISHIDA Takashi, AKIYAMA Yutaka, SEKIJIMA Masakazu, OHNO Kazuki, ORITA Masaya

The quarterly journal of Ritsumeikan University   52 ( 2 )   267 - 282   2013.11

Improvement of drug clearance pathway prediction using binding free energy calculation

SAITO YUKI, ISHIDA TAKASHI, SEKIJIMA MASAKAZU, AKIYAMA YUTAKA

IEICE technical report. Neurocomputing   113 ( 111 )   83 - 88   2013.6

Evaluation of Sparse k-mer graph algorithm and its implementation on Velvet

YOSHIKAWA SHUNSUKE, ISHIDA TAKASHI, SEKIJIMA MASAKAZU, AKIYAMA YUTAKA

IEICE technical report. Neurocomputing   113 ( 111 )   1 - 7   2013.6

Characterizing Delaunay Graphs via Fixed Point Theorem

2012 ( 24 )   1 - 3   2012.11

Inprovement of Velvet by dividing PreGraph

2012 ( 24 )   1 - 3   2012.11

De novo sequence assembly based on divided hash tables

SUGIURA NORIKAZU, ISHIDA TAKASHI, SEKIJIMA MASAKAZU, AKIYAMA YUTAKA

IEICE technical report. Neurocomputing   112 ( 108 )   133 - 139   2012.6

De novo sequence assembly based on divided hash tables

2012 ( 25 )   1 - 7   2012.6