Zobrazeno 1 - 10
of 44
pro vyhledávání: '"Rafał Ślusarz"'
Publikováno v:
Frontiers in Molecular Biosciences, Vol 9 (2022)
In this paper we report the improvements and extensions of the UNRES server (https://unres-server.chem.ug.edu.pl) for physics-based simulations with the coarse-grained UNRES model of polypeptide chains. The improvements include the replacement of the
Externí odkaz:
https://doaj.org/article/3704a2487bc146ac996f336327ff6dd8
Autor:
Rafał Ślusarz, Barbara Dmochowska, Justyna Samaszko-Fiertek, Krzysztof Brzozowski, Janusz Madaj
Publikováno v:
International Journal of Molecular Sciences, Vol 23, Iss 3, p 1146 (2022)
The article describes an NMR spectroscopy study of interactions between vancomycin and a muramyl pentapeptide in two complexes: vancomycin and a native muramyl pentapeptide ended with D-alanine (MPP-D-Ala), and vancomycin and a modified muramyl penta
Externí odkaz:
https://doaj.org/article/b832210e66a84f359610f29a0152a574
Autor:
Barbara Dmochowska, Rafał Ślusarz, Jarosław Chojnacki, Justyna Samaszko-Fiertek, Janusz Madaj
Publikováno v:
Molecules, Vol 25, Iss 9, p 2161 (2020)
The synthesis of N-((methyl 5-deoxy-2,3-O-isopropylidene-β-D-ribofuranoside)-5-yl)ammonium salts are presented. To determine the effect of the nucleophile type and outgoing group on the quaternization reaction, selected aliphatic and heterocyclic ar
Externí odkaz:
https://doaj.org/article/289f6f948d0546309eb3d7b6caef3d03
Autor:
Barbara Dmochowska, Monika Szulc, Wojciech Kamysz, Maciej Jaśkiewicz, J. Samaszko-Fiertek, Rafał Ślusarz, Janusz Madaj
Publikováno v:
Letters in Organic Chemistry. 17:287-293
This paper presents synthesis of vancomycin derivatives modified with selected 1- and 2-aminoalditols to carboxylic function and 2,5-anhydro-D-mannose and D-talose to amino function of vancosamine via reductive alkylation. MIC and MBC of these deriva
Autor:
Agnieszka S. Karczyńska, Agnieszka G. Lipska, Adam Liwo, Artur Giełdoń, Adam K. Sieradzan, Silvia Crivelli, Karolina Ziȩba, Łukasz Golon, Magdalena A. Mozolewska, Urszula Uciechowska, Sergey A. Samsonov, Magdalena J. Ślusarz, Paweł Krupa, Emilia A. Lubecka, Rafał Ślusarz, Cezary Czaplewski, Celina Sikorska
Publikováno v:
Journal of Molecular Graphics and Modelling. 92:154-166
The recent NEWCT-9P version of the coarse-grained UNRES force field for proteins, with scale-consistent formulas for the local and correlation terms, has been tested in the CASP13 experiment of the blind-prediction of protein structure, in the ab ini
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:
Cezary Czaplewski, Rafał Ślusarz, Iga Biskupek, Mateusz Kogut, Martyna Maszota-Zieleniak, Agnieszka G. Lipska, Mateusz Marcisz, Emilia A. Lubecka, Magdalena J. Ślusarz, Adam Liwo, Adam K. Sieradzan, Anna Antoniak, Małgorzata M. Kogut, Patryk A. Wesołowski, Krzysztof K. Bojarski, Sergey A. Samsonov, Karolina Ziȩba, Artur Giełdoń, Paweł Krupa
Publikováno v:
Journal of molecular graphicsmodelling. 108
The UNited RESidue (UNRES) force field was tested in the 14th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP14), in which larger oligomeric and multimeric targets were present compared to pre
Autor:
Rafał Ślusarz, Cezary Czaplewski, Magdalena J. Ślusarz, Adam Liwo, Adam K. Sieradzan, Karolina Ziȩba
Publikováno v:
The Journal of Physical Chemistry B. 123:7829-7839
The physics-based UNRES coarse-grained force field for the simulations of protein structure and dynamics has been extended to treat membrane proteins. The lipid bilayer has been modeled by introducing a continuous nonpolar phase with the water-interf
Autor:
Karolina Ziȩba, Emilia A. Lubecka, Jooyoung Lee, Sergey A. Samsonov, Agnieszka S. Karczyńska, Cezary Czaplewski, Magdalena A. Mozolewska, Urszula Uciechowska, Agnieszka G. Lipska, Adam Liwo, Keehyoung Joo, Adam K. Sieradzan, Magdalena J. Ślusarz, Rafał Ślusarz, Paweł Krupa, Artur Giełdoń, Celina Sikorska
Publikováno v:
Journal of Chemical Information and Modeling
The method for protein-structure prediction, which combines the physics-based coarse-grained UNRES force field with knowledge-based modeling, has been developed further and tested in the 13th Community Wide Experiment on the Critical Assessment of Te