Zobrazeno 1 - 10
of 12
pro vyhledávání: '"Jacob Verburgt"'
Autor:
R Shyama Prasad Rao, Nagib Ahsan, Chunhui Xu, Lingtao Su, Jacob Verburgt, Luca Fornelli, Daisuke Kihara, Dong Xu
Publikováno v:
Evolutionary Bioinformatics, Vol 17 (2021)
SARS-CoV-2, responsible for the current COVID-19 pandemic that claimed over 5.0 million lives, belongs to a class of enveloped viruses that undergo quick evolutionary adjustments under selection pressure. Numerous variants have emerged in SARS-CoV-2,
Externí odkaz:
https://doaj.org/article/c3613700973d496e97b70f052c993bc5
Autor:
Jose L. Olmos, Suraj Pandey, Jose M. Martin-Garcia, George Calvey, Andrea Katz, Juraj Knoska, Christopher Kupitz, Mark S. Hunter, Mengning Liang, Dominik Oberthuer, Oleksandr Yefanov, Max Wiedorn, Michael Heyman, Mark Holl, Kanupriya Pande, Anton Barty, Mitchell D. Miller, Stephan Stern, Shatabdi Roy-Chowdhury, Jesse Coe, Nirupa Nagaratnam, James Zook, Jacob Verburgt, Tyler Norwood, Ishwor Poudyal, David Xu, Jason Koglin, Matthew H. Seaberg, Yun Zhao, Saša Bajt, Thomas Grant, Valerio Mariani, Garrett Nelson, Ganesh Subramanian, Euiyoung Bae, Raimund Fromme, Russell Fung, Peter Schwander, Matthias Frank, Thomas A. White, Uwe Weierstall, Nadia Zatsepin, John Spence, Petra Fromme, Henry N. Chapman, Lois Pollack, Lee Tremblay, Abbas Ourmazd, George N. Phillips, Marius Schmidt
Publikováno v:
BMC Biology, Vol 16, Iss 1, Pp 1-15 (2018)
Abstract Background Ever since the first atomic structure of an enzyme was solved, the discovery of the mechanism and dynamics of reactions catalyzed by biomolecules has been the key goal for the understanding of the molecular processes that drive li
Externí odkaz:
https://doaj.org/article/cc4fc7b9369349448afd757a6952a22b
Autor:
Daisuke Kihara, Jacob Verburgt
Publikováno v:
Proteins
Protein structure docking is the process in which the quaternary structure of a protein complex is predicted from individual tertiary structures of the protein subunits. Protein docking is typically performed in two main steps. The subunits are first
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::64d2f5a29c77f38d02f47a5c1c007b7c
https://doi.org/10.1002/prot.26188
https://doi.org/10.1002/prot.26188
Publikováno v:
Methods (San Diego, Calif.). 204
Intrinsically Disordered Proteins (IDPs) are a class of proteins in which at least some region of the protein does not possess any stable structure in solution in the physiological condition but may adopt an ordered structure upon binding to a globul
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::b71f0cc420af13aa5cd195c502753fd1
https://pubmed.ncbi.nlm.nih.gov/35609776
https://pubmed.ncbi.nlm.nih.gov/35609776
Autor:
Xiaoqin Zou, Théo Mauri, Hang Shi, Shaowen Zhu, Justas Dapkūnas, Yuanfei Sun, Didier Barradas-Bautista, Raphael A. G. Chaleil, Ragul Gowthaman, Sohee Kwon, Xianjin Xu, Zuzana Jandova, Genki Terashi, Ryota Ashizawa, Petras J. Kundrotas, Shuang Zhang, Tunde Aderinwale, Jian Liu, Sandor Vajda, Paul A. Bates, Jianlin Cheng, Daisuke Kihara, Luis A. Rodríguez-Lumbreras, Carlos A. Del Carpio Muñoz, Liming Qiu, Guillaume Brysbaert, Jorge Roel-Touris, Česlovas Venclovas, Tereza Clarence, Rui Yin, Amar Singh, Patryk A. Wesołowski, Rafał Ślusarz, Adam Liwo, Guangbo Yang, Agnieszka S. Karczyńska, Yoshiki Harada, Sergei Kotelnikov, Yuya Hanazono, Charlotte W. van Noort, Marc F. Lensink, Jonghun Won, Adam K. Sieradzan, Israel Desta, Xufeng Lu, Charles Christoffer, Anna Antoniak, Taeyong Park, Sheng-You Huang, Tsukasa Nakamura, Brian G. Pierce, Usman Ghani, Yang Shen, Luigi Cavallo, Chaok Seok, Hao Li, Nurul Nadzirin, Ghazaleh Taherzadeh, Jacob Verburgt, Rodrigo V. Honorato, Artur Giełdoń, Jeffrey J. Gray, Dima Kozakov, Ming Liu, Shan Chang, Eiichiro Ichiishi, Manon Réau, Rui Duan, Francesco Ambrosetti, Johnathan D. Guest, Juan Fernández-Recio, Alexandre M. J. J. Bonvin, Ilya A. Vakser, Farhan Quadir, Yumeng Yan, Ren Kong, Sameer Velankar, Sergei Grudinin, Mateusz Kogut, Mikhail Ignatov, Yasuomi Kiyota, Hyeonuk Woo, Shoshana J. Wodak, Ameya Harmalkar, Shinpei Kobayashi, Panagiotis I. Koukos, Zhen Cao, Kliment Olechnovič, Cezary Czaplewski, Xiao Wang, Agnieszka G. Lipska, Kathryn A. Porter, Peicong Lin, Emilia A. Lubecka, Nasser Hashemi, Bin Liu, Mayuko Takeda-Shitaka, Karolina Zięba, Dzmitry Padhorny, Zhuyezi Sun, Daipayan Sarkar, Romina Oliva, Andrey Alekseenko, Siri Camee van Keulen, Mireia Rosell, Raj S. Roy, Brian Jiménez-García, Jinsol Yang, Martyna Maszota-Zieleniak
Publikováno v:
Proteins: Structure, Function and Bioinformatics, 89(12), 1800. Wiley-Liss Inc.
Proteins-Structure, Function and Bioinformatics
Proteins-Structure, Function and Bioinformatics, Wiley, 2021, ⟨10.1002/prot.26222⟩
Digital.CSIC. Repositorio Institucional del CSIC
instname
Proteins
Proteins-Structure, Function and Bioinformatics, 2021, 89 (12), pp.1800-1823. ⟨10.1002/prot.26222⟩
Proteins-Structure, Function and Bioinformatics
Proteins-Structure, Function and Bioinformatics, Wiley, 2021, ⟨10.1002/prot.26222⟩
Digital.CSIC. Repositorio Institucional del CSIC
instname
Proteins
Proteins-Structure, Function and Bioinformatics, 2021, 89 (12), pp.1800-1823. ⟨10.1002/prot.26222⟩
We present the results for CAPRI Round 50, the fourth joint CASP-CAPRI protein assembly prediction challenge. The Round comprised a total of twelve targets, including six dimers, three trimers, and three higher-order oligomers. Four of these were eas
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::8f1657fc608b7d209e1b9345caf8b2fb
https://dspace.library.uu.nl/handle/1874/417637
https://dspace.library.uu.nl/handle/1874/417637
Autor:
Yumeng Yan, Mateusz Kogut, Sohee Kwon, Israel Desta, Petras J. Kundrotas, Xiaoqin Zou, Xiao Wang, Dima Kozakov, Eiichiro Ichiishi, Kathryn A. Porter, Johnathan D. Guest, Brian G. Pierce, Daisuke Kihara, Česlovas Venclovas, Agnieszka G. Lipska, Luigi Cavallo, Panagiotis I. Koukos, Yang Shen, Ren Kong, Brian Jiménez-García, Kliment Olechnovič, Cezary Czaplewski, Peicong Lin, Sameer Velankar, Shoshana J. Wodak, Agnieszka S. Karczyńska, Emilia A. Lubecka, Mikhail Ignatov, Shan Chang, Daipayan Sarkar, Sheng-You Huang, Chaok Seok, Nurul Nadzirin, Hao Li, Anna Antoniak, Manon Réau, Hyeonuk Woo, Siri Camee van Keulen, Ryota Ashizawa, Nasser Hashemi, Adam Liwo, Zhen Cao, Yoshiki Harada, Genki Terashi, Ameya Harmalkar, Farhan Quadir, Shinpei Kobayashi, Sandor Vajda, Zuzana Jandova, Juan Fernández-Recio, Amar Singh, Martyna Maszota-Zieleniak, Rodrigo V. Honorato, Usman Ghani, Sergei Grudinin, Xufeng Lu, Jorge Roel-Touris, Ming Liu, Paul A. Bates, Ghazaleh Taherzadeh, Adam K. Sieradzan, Patryk A. Wesołowski, Théo Mauri, Ilya A. Vakser, Francesco Ambrosetti, Jinsol Yang, Sergei Kotelnikov, Hang Shi, Shuang Zhang, Marc F. Lensink, Justas Dapkūnas, Yasuomi Kiyota, Taeyong Park, Mayuko Takeda-Shitaka, Andrey Alekseenko, Jian Liu, Artur Giełdoń, Ragul Gowthaman, Jonghun Won, Tsukasa Nakamura, Tunde Aderinwale, Yuanfei Sun, Guillaume Brysbaert, Jeffrey J. Gray, Luis A. Rodríguez-Lumbreras, Yuya Hanazono, Charlotte W. van Noort, Carlos A. Del Carpio Muñoz, Rui Duan, Alexandre M. J. J. Bonvin, Jianlin Cheng, Liming Qiu, Tereza Clarence, Rui Yin, Guangbo Yang, Shaowen Zhu, Didier Barradas-Bautista, Rafał Ślusarz, Raphael A. G. Chaleil, Charles Christoffer, Jacob Verburgt, Dzmitry Padhorny, Zhuyezi Sun, Romina Oliva, Mireia Rosell, Raj S. Roy, Bin Liu, Karolina Zięba
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::4ef61647ab31e6706772c0fd1df032b4
https://doi.org/10.1002/prot.26222/v2/response1
https://doi.org/10.1002/prot.26222/v2/response1
Autor:
Max Petersen, M. Ruhul Abid, Ujwal Punyamurtula, R. Shyama Prasad Rao, Rashaun S. Wilson, Mohammad Kabir Ahmed, Zhibo Yang, Daisuke Kihara, Bharat Ramratnam, Steven B. Foster, Fernanda Salvato, Luca Fornelli, Nagib Ahsan, Jacob Verburgt
Publikováno v:
Proteomics
While protein–protein interaction is the first step of the SARS‐CoV‐2 infection, recent comparative proteomic profiling enabled the identification of over 11,000 protein dynamics, thus providing a comprehensive reflection of the molecular mecha
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4f1bae548a573c022147ada5905778db
http://europepmc.org/articles/PMC8250252
http://europepmc.org/articles/PMC8250252
Autor:
Charles Christoffer, Daisuke Kihara, Jacob Verburgt, Lenna X. Peterson, Woong-Hee Shin, Genki Terashi, Sai Raghavendra Maddhuri Venkata Subramaniya, Tunde Aderinwale
Publikováno v:
Proteins
We report the performance of the protein docking prediction pipeline of our group and the results for Critical Assessment of Prediction of Interactions (CAPRI) rounds 38-46. The pipeline integrates programs developed in our group as well as other exi
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::1e4b2b152e18a6ee81458f7acd2911d3
https://pubmed.ncbi.nlm.nih.gov/31697428
https://pubmed.ncbi.nlm.nih.gov/31697428
Autor:
Chunhui Xu, Nagib Ahsan, R. Shyama Prasad Rao, Dong Xu, Lingtao Su, Luca Fornelli, Daisuke Kihara, Jacob Verburgt
Publikováno v:
Evolutionary Bioinformatics, Vol 17 (2021)
Evolutionary Bioinformatics
Evolutionary Bioinformatics
SARS-CoV-2, responsible for the current COVID-19 pandemic that claimed over 4.2 million lives, belongs to a class of enveloped viruses that undergo quick evolutionary adjustments under selection pressure. Numerous variants have emerged in SARS-CoV-2
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::394bbff78ea8e3460be43c880b734d04
https://doi.org/10.1177/11769343211064616
https://doi.org/10.1177/11769343211064616