Genki Terashi

Affiliations

Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.

ORCID: 0000-0002-5339-909X

Publications (16)

VESPER: global and local cryo-EM map alignment using local density vectors.

Nature communications

Avec: Xusi Han , Genki Terashi , Charles Christoffer , Siyang Chen , Daisuke Kihara

Performance and enhancement of the LZerD protein assembly pipeline in CAPRI 38-46.

Proteins

Avec: Charles Christoffer , Genki Terashi , Woong-Hee Shin , Tunde Aderinwale , Sai Raghavendra Maddhuri Venkata Subramaniya , Lenna Peterson , Jacob Verburgt , Daisuke Kihara

MAINMASTseg: Automated Map Segmentation Method for Cryo-EM Density Maps with Symmetry.

Journal of chemical information and modeling

Avec: Genki Terashi , Yuki Kagaya , Daisuke Kihara

Efficient Flexible Fitting Refinement with Automatic Error Fixing for De Novo Structure Modeling from Cryo-EM Density Maps.

Journal of chemical information and modeling

Avec: Takaharu Mori , Genki Terashi , Daisuke Matsuoka , Daisuke Kihara , Yuji Sugita

Unveiling the stochastic nature of human heteropolymer ferritin self-assembly mechanism.

Protein science : a publication of the Protein Society

Avec: Fadi Bou-Abdallah , Jeremie Fish , Genki Terashi , Yuanyuan Zhang , Daisuke Kihara , Paolo Arosio

MarkovFit: Structure Fitting for Protein Complexes in Electron Microscopy Maps Using Markov Random Field.

Frontiers in molecular biosciences

Avec: Eman Alnabati , Juan Esquivel-Rodriguez , Genki Terashi , Daisuke Kihara

Path-LZerD: Predicting Assembly Order of Multimeric Protein Complexes.

Methods in molecular biology (Clifton, N.J.)

Avec: Genki Terashi , Charles Christoffer , Daisuke Kihara

Protein contact map refinement for improving structure prediction using generative adversarial networks.

Bioinformatics (Oxford, England)

Avec: Sai Raghavendra Maddhuri Venkata Subramaniya , Genki Terashi , Aashish Jain , Yuki Kagaya , Daisuke Kihara

Real-time structure search and structure classification for AlphaFold protein models.

Communications biology

Avec: Tunde Aderinwale , Vijay Bharadwaj , Charles Christoffer , Genki Terashi , Zicong Zhang , Rashidedin Jahandideh , Yuki Kagaya , Daisuke Kihara

Enhancing cryo-EM maps with 3D deep generative networks for assisting protein structure modeling.

Bioinformatics (Oxford, England)

Avec: Sai Raghavendra Maddhuri Venkata Subramaniya , Genki Terashi , Daisuke Kihara

Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment.

Proteins

Avec: Marc F Lensink , Guillaume Brysbaert , Nessim Raouraoua , Paul A Bates , Marco Giulini , Rodrigo V Honorato , Charlotte van Noort , Joao M C Teixeira , Alexandre M J J Bonvin , Ren Kong , Hang Shi , Xufeng Lu , Shan Chang , Jian Liu , Zhiye Guo , Xiao Chen , Alex Morehead , Raj S Roy , Tianqi Wu , Nabin Giri , Farhan Quadir , Chen Chen , Jianlin Cheng , Carlos A Del Carpio , Eichiro Ichiishi , Luis A Rodriguez-Lumbreras , Juan Fernandez-Recio , Ameya Harmalkar , Lee-Shin Chu , Sam Canner , Rituparna Smanta , Jeffrey J Gray , Hao Li , Peicong Lin , Jiahua He , Huanyu Tao , Sheng-You Huang , Jorge Roel-Touris , Brian Jimenez-Garcia , Charles W Christoffer , Anika J Jain , Yuki Kagaya , Harini Kannan , Tsukasa Nakamura , Genki Terashi , Jacob C Verburgt , Yuanyuan Zhang , Zicong Zhang , Hayato Fujuta , Masakazu Sekijima , Daisuke Kihara , Omeir Khan , Sergei Kotelnikov , Usman Ghani , Dzmitry Padhorny , Dmitri Beglov , Sandor Vajda , Dima Kozakov , Surendra S Negi , Tiziana Ricciardelli , Didier Barradas-Bautista , Zhen Cao , Mohit Chawla , Luigi Cavallo , Romina Oliva , Rui Yin , Melyssa Cheung , Johnathan D Guest , Jessica Lee , Brian G Pierce , Ben Shor , Tomer Cohen , Matan Halfon , Dina Schneidman-Duhovny , Shaowen Zhu , Rujie Yin , Yuanfei Sun , Yang Shen , Martyna Maszota-Zieleniak , Krzysztof K Bojarski , Emilia A Lubecka , Mateusz Marcisz , Annemarie Danielsson , Lukasz Dziadek , Margrethe Gaardlos , Artur Gieldon , Adam Liwo , Sergey A Samsonov , Rafal Slusarz , Karolina Zieba , Adam K Sieradzan , Cezary Czaplewski , Shinpei Kobayashi , Yuta Miyakawa , Yasuomi Kiyota , Mayuko Takeda-Shitaka , Kliment Olechnovic , Lukas Valancauskas , Justas Dapkunas , Ceslovas Venclovas , Bjorn Wallner , Lin Yang , Chengyu Hou , Xiaodong He , Shuai Guo , Shenda Jiang , Xiaoliang Ma , Rui Duan , Liming Qui , Xianjin Xu , Xiaoqin Zou , Sameer Velankar , Shoshana J Wodak

Bioinformatic Approaches for Characterizing Molecular Structure and Function of Food Proteins.

Annual review of food science and technology

Avec: Harrison Helmick , Anika Jain , Genki Terashi , Andrea Liceaga , Arun K Bhunia , Daisuke Kihara , Jozef L Kokini

Outcomes of the EMDataResource Cryo-EM Ligand Modeling Challenge.

Research square

Avec: Catherine Lawson , Andriy Kryshtafovych , Grigore Pintilie , Stephen Burley , Jiri Cerny , Vincent Chen , Paul Emsley , Alberto Gobbi , Andrzej Joachimiak , Sigrid Noreng , Michael Prisant , Randy Read , Jane Richardson , Alexis Rohou , Bohdan Schneider , Benjamin Sellers , Chenghua Chao , Elizabeth Sourial , Chris Williams , Christopher Williams , Ying Yang , Venkat Abbaraju , Pavel V Afonine , Matthew Baker , Paul Bond , Tom Blundell , Tom Burnley , Arthur Campbell , Renzhi Cao , Jianlin Cheng , Grzegorz Chojnowski , Kevin Cowtan , Frank Dimaio , Reza Esmaeeli , Nabin Giri , Helmut Grubmüller , Soon Wen Hoh , Jie Hou , Corey Hryc , Carola Hunte , Maxim Igaev , Agnel Joseph , Wei-Chun Kao , Daisuke Kihara , Dilip Kumar , Lijun Lang , Sean Lin , Sai Raghavendra Maddhuri Venkata Subramaniya , Sumit Mittal , Arup Mondal , Nigel Moriarty , Andrew Muenks , Garib Murshudov , Robert Nicholls , Mateusz Olek , Colin Palmer , Alberto Perez , Emmi Pohjolainen , Karunakar Pothula , Christopher Rowley , Daipayan Sarkar , Luisa Schäfer , Christopher Schlicksup , Gunnar Schroeder , Mrinal Shekhar , Dong Si , Abhishek Singharoy , Oleg Sobolev , Genki Terashi , Andrea Vaiana , Sundeep Vedithi , Jacob Verburgt , Xiao Wang , Rangana Warshamanage , Martyn Winn , Simone Weyand , Keitaro Yamashita , Minglei Zhao , Michael Schmid , Helen Berman , Wah Chiu

DiffModeler: Large Macromolecular Structure Modeling in Low-Resolution Cryo-EM Maps Using Diffusion Model.

bioRxiv : the preprint server for biology

Avec: Xiao Wang , Han Zhu , Genki Terashi , Manav Taluja , Daisuke Kihara

Analyzing effect of quadruple multiple sequence alignments on deep learning based protein inter-residue distance prediction.

Scientific reports

Avec: Aashish Jain , Genki Terashi , Yuki Kagaya , Sai Raghavendra Maddhuri Venkata Subramaniya , Charles Christoffer , Daisuke Kihara

Discriminating physiological from non-physiological interfaces in structures of protein complexes: A community-wide study.

Proteomics

Avec: Hugo Schweke , Qifang Xu , Gerardo Tauriello , Lorenzo Pantolini , Torsten Schwede , Frédéric Cazals , Alix Lhéritier , Juan Fernandez-Recio , Luis Angel Rodríguez-Lumbreras , Ora Schueler-Furman , Julia K Varga , Brian Jiménez-García , Manon F Réau , Alexandre M J J Bonvin , Castrense Savojardo , Pier-Luigi Martelli , Rita Casadio , Jérôme Tubiana , Haim J Wolfson , Romina Oliva , Didier Barradas-Bautista , Tiziana Ricciardelli , Luigi Cavallo , Česlovas Venclovas , Kliment Olechnovič , Raphael Guerois , Jessica Andreani , Juliette Martin , Xiao Wang , Genki Terashi , Daipayan Sarkar , Charles Christoffer , Tunde Aderinwale , Jacob Verburgt , Daisuke Kihara , Anthony Marchand , Bruno E Correia , Rui Duan , Liming Qiu , Xianjin Xu , Shuang Zhang , Xiaoqin Zou , Sucharita Dey , Roland L Dunbrack , Emmanuel D Levy , Shoshana J Wodak

Réseau de co-auteurs

Daisuke Kihara 16 collaborations

Charles Christoffer 6 collaborations

Sai Raghavendra Maddhuri Venkata Subramaniya 5 collaborations

Yuki Kagaya 5 collaborations

Tunde Aderinwale 3 collaborations

Jacob Verburgt 3 collaborations

Xiao Wang 3 collaborations

Yuanyuan Zhang 2 collaborations

Aashish Jain 2 collaborations

Zicong Zhang 2 collaborations

Alexandre M J J Bonvin 2 collaborations

Nabin Giri 2 collaborations

Jianlin Cheng 2 collaborations

Juan Fernandez-Recio 2 collaborations

Tiziana Ricciardelli 2 collaborations

Didier Barradas-Bautista 2 collaborations

Luigi Cavallo 2 collaborations

Romina Oliva 2 collaborations

Rui Duan 2 collaborations

Xianjin Xu 2 collaborations

Xiaoqin Zou 2 collaborations

Shoshana J Wodak 2 collaborations

Daipayan Sarkar 2 collaborations

Xusi Han 1 collaboration

Siyang Chen 1 collaboration

Woong-Hee Shin 1 collaboration

Lenna Peterson 1 collaboration

Takaharu Mori 1 collaboration

Daisuke Matsuoka 1 collaboration

Yuji Sugita 1 collaboration

Fadi Bou-Abdallah 1 collaboration

Jeremie Fish 1 collaboration

Paolo Arosio 1 collaboration

Eman Alnabati 1 collaboration

Juan Esquivel-Rodriguez 1 collaboration

Vijay Bharadwaj 1 collaboration

Rashidedin Jahandideh 1 collaboration

Marc F Lensink 1 collaboration

Guillaume Brysbaert 1 collaboration

Nessim Raouraoua 1 collaboration

Paul A Bates 1 collaboration

Marco Giulini 1 collaboration

Rodrigo V Honorato 1 collaboration

Charlotte van Noort 1 collaboration

Joao M C Teixeira 1 collaboration

Ren Kong 1 collaboration

Hang Shi 1 collaboration

Xufeng Lu 1 collaboration

Shan Chang 1 collaboration

Jian Liu 1 collaboration

Zhiye Guo 1 collaboration

Xiao Chen 1 collaboration

Alex Morehead 1 collaboration

Raj S Roy 1 collaboration

Tianqi Wu 1 collaboration

Farhan Quadir 1 collaboration

Chen Chen 1 collaboration

Carlos A Del Carpio 1 collaboration

Eichiro Ichiishi 1 collaboration

Luis A Rodriguez-Lumbreras 1 collaboration

Ameya Harmalkar 1 collaboration

Lee-Shin Chu 1 collaboration

Sam Canner 1 collaboration

Rituparna Smanta 1 collaboration

Jeffrey J Gray 1 collaboration

Hao Li 1 collaboration

Peicong Lin 1 collaboration

Jiahua He 1 collaboration

Huanyu Tao 1 collaboration

Sheng-You Huang 1 collaboration

Jorge Roel-Touris 1 collaboration

Brian Jimenez-Garcia 1 collaboration

Charles W Christoffer 1 collaboration

Anika J Jain 1 collaboration

Harini Kannan 1 collaboration

Tsukasa Nakamura 1 collaboration

Jacob C Verburgt 1 collaboration

Hayato Fujuta 1 collaboration

Masakazu Sekijima 1 collaboration

Omeir Khan 1 collaboration

Sergei Kotelnikov 1 collaboration

Usman Ghani 1 collaboration

Dzmitry Padhorny 1 collaboration

Dmitri Beglov 1 collaboration

Sandor Vajda 1 collaboration

Dima Kozakov 1 collaboration

Surendra S Negi 1 collaboration

Zhen Cao 1 collaboration

Mohit Chawla 1 collaboration

Rui Yin 1 collaboration

Melyssa Cheung 1 collaboration

Johnathan D Guest 1 collaboration

Jessica Lee 1 collaboration

Brian G Pierce 1 collaboration

Ben Shor 1 collaboration

Tomer Cohen 1 collaboration

Matan Halfon 1 collaboration

Dina Schneidman-Duhovny 1 collaboration

Shaowen Zhu 1 collaboration

Rujie Yin 1 collaboration

Yuanfei Sun 1 collaboration

Yang Shen 1 collaboration

Martyna Maszota-Zieleniak 1 collaboration

Krzysztof K Bojarski 1 collaboration

Emilia A Lubecka 1 collaboration

Mateusz Marcisz 1 collaboration

Annemarie Danielsson 1 collaboration

Lukasz Dziadek 1 collaboration

Margrethe Gaardlos 1 collaboration

Artur Gieldon 1 collaboration

Adam Liwo 1 collaboration

Sergey A Samsonov 1 collaboration

Rafal Slusarz 1 collaboration

Karolina Zieba 1 collaboration

Adam K Sieradzan 1 collaboration

Cezary Czaplewski 1 collaboration

Shinpei Kobayashi 1 collaboration

Yuta Miyakawa 1 collaboration

Yasuomi Kiyota 1 collaboration

Mayuko Takeda-Shitaka 1 collaboration

Kliment Olechnovic 1 collaboration

Lukas Valancauskas 1 collaboration

Justas Dapkunas 1 collaboration

Ceslovas Venclovas 1 collaboration

Bjorn Wallner 1 collaboration

Lin Yang 1 collaboration

Chengyu Hou 1 collaboration

Xiaodong He 1 collaboration

Shuai Guo 1 collaboration

Shenda Jiang 1 collaboration

Xiaoliang Ma 1 collaboration

Liming Qui 1 collaboration

Sameer Velankar 1 collaboration

Harrison Helmick 1 collaboration

Anika Jain 1 collaboration

Andrea Liceaga 1 collaboration

Arun K Bhunia 1 collaboration

Jozef L Kokini 1 collaboration

Catherine Lawson 1 collaboration

Andriy Kryshtafovych 1 collaboration

Grigore Pintilie 1 collaboration

Stephen Burley 1 collaboration

Jiri Cerny 1 collaboration

Vincent Chen 1 collaboration

Paul Emsley 1 collaboration

Alberto Gobbi 1 collaboration

Andrzej Joachimiak 1 collaboration

Sigrid Noreng 1 collaboration

Michael Prisant 1 collaboration

Randy Read 1 collaboration

Jane Richardson 1 collaboration

Alexis Rohou 1 collaboration

Bohdan Schneider 1 collaboration

Benjamin Sellers 1 collaboration

Chenghua Chao 1 collaboration

Elizabeth Sourial 1 collaboration

Chris Williams 1 collaboration

Christopher Williams 1 collaboration

Ying Yang 1 collaboration

Venkat Abbaraju 1 collaboration

Pavel V Afonine 1 collaboration

Matthew Baker 1 collaboration

Paul Bond 1 collaboration

Tom Blundell 1 collaboration

Tom Burnley 1 collaboration

Arthur Campbell 1 collaboration

Renzhi Cao 1 collaboration

Grzegorz Chojnowski 1 collaboration

Kevin Cowtan 1 collaboration

Frank Dimaio 1 collaboration

Reza Esmaeeli 1 collaboration

Helmut Grubmüller 1 collaboration

Soon Wen Hoh 1 collaboration

Jie Hou 1 collaboration

Corey Hryc 1 collaboration

Carola Hunte 1 collaboration

Maxim Igaev 1 collaboration

Agnel Joseph 1 collaboration

Wei-Chun Kao 1 collaboration

Dilip Kumar 1 collaboration

Lijun Lang 1 collaboration

Sean Lin 1 collaboration

Sumit Mittal 1 collaboration

Arup Mondal 1 collaboration

Nigel Moriarty 1 collaboration

Andrew Muenks 1 collaboration

Garib Murshudov 1 collaboration

Robert Nicholls 1 collaboration

Mateusz Olek 1 collaboration

Colin Palmer 1 collaboration

Alberto Perez 1 collaboration

Emmi Pohjolainen 1 collaboration

Karunakar Pothula 1 collaboration

Christopher Rowley 1 collaboration

Luisa Schäfer 1 collaboration

Christopher Schlicksup 1 collaboration

Gunnar Schroeder 1 collaboration

Mrinal Shekhar 1 collaboration

Dong Si 1 collaboration

Abhishek Singharoy 1 collaboration

Oleg Sobolev 1 collaboration

Andrea Vaiana 1 collaboration

Sundeep Vedithi 1 collaboration

Rangana Warshamanage 1 collaboration

Martyn Winn 1 collaboration

Simone Weyand 1 collaboration

Keitaro Yamashita 1 collaboration

Minglei Zhao 1 collaboration

Michael Schmid 1 collaboration

Helen Berman 1 collaboration

Wah Chiu 1 collaboration

Han Zhu 1 collaboration

Manav Taluja 1 collaboration

Hugo Schweke 1 collaboration

Qifang Xu 1 collaboration

Gerardo Tauriello 1 collaboration

Lorenzo Pantolini 1 collaboration

Torsten Schwede 1 collaboration

Frédéric Cazals 1 collaboration

Alix Lhéritier 1 collaboration

Luis Angel Rodríguez-Lumbreras 1 collaboration

Ora Schueler-Furman 1 collaboration

Julia K Varga 1 collaboration

Brian Jiménez-García 1 collaboration

Manon F Réau 1 collaboration

Castrense Savojardo 1 collaboration

Pier-Luigi Martelli 1 collaboration

Rita Casadio 1 collaboration

Jérôme Tubiana 1 collaboration

Haim J Wolfson 1 collaboration

Česlovas Venclovas 1 collaboration

Kliment Olechnovič 1 collaboration

Raphael Guerois 1 collaboration

Jessica Andreani 1 collaboration

Juliette Martin 1 collaboration

Anthony Marchand 1 collaboration

Bruno E Correia 1 collaboration

Liming Qiu 1 collaboration

Shuang Zhang 1 collaboration

Sucharita Dey 1 collaboration

Roland L Dunbrack 1 collaboration

Emmanuel D Levy 1 collaboration