Zobrazeno 1 - 10
of 343
pro vyhledávání: '"Adam, Liwo"'
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
Publikováno v:
Biomolecules, Vol 13, Iss 6, p 941 (2023)
Molecular motors are essential for the movement and transportation of macromolecules in living organisms. Among them, rotatory motors are particularly efficient. In this study, we investigated the long-term dynamics of the designed left-handed alpha/
Externí odkaz:
https://doaj.org/article/bc5e920880a34a19b1ae31af38e0ccbc
Autor:
Frank Gondelaud, Mathilde Bouakil, Aurélien Le Fèvre, Adriana Erica Miele, Fabien Chirot, Bertrand Duclos, Adam Liwo, Sylvie Ricard-Blum
Publikováno v:
Matrix Biology Plus, Vol 12, Iss , Pp 100081- (2021)
Syndecans are membrane proteoglycans regulating extracellular matrix assembly, cell adhesion and signaling. Their ectodomains can be shed from the cell surface, and act as paracrine and autocrine effectors or as competitors of full-length syndecans.
Externí odkaz:
https://doaj.org/article/62832c02c9af4663a3d186689846b84d
Publikováno v:
Frontiers in Molecular Biosciences, Vol 8 (2021)
Many proteins can fold into well-defined conformations. However, intrinsically-disordered proteins (IDPs) do not possess a defined structure. Moreover, folded multi-domain proteins often digress into alternative conformations. Collectively, the confo
Externí odkaz:
https://doaj.org/article/6e60b07e33744aae96ee6cff26c2e30d
Autor:
Iga Biskupek, Cezary Czaplewski, Justyna Sawicka, Emilia Iłowska, Maria Dzierżyńska, Sylwia Rodziewicz-Motowidło, Adam Liwo
Publikováno v:
Biomolecules, Vol 12, Iss 8, p 1140 (2022)
The UNited RESidue (UNRES) model of polypeptide chains was applied to study the association of 20 peptides with sizes ranging from 6 to 32 amino-acid residues. Twelve of those were potentially aggregating hexa- or heptapeptides excised from larger pr
Externí odkaz:
https://doaj.org/article/1611e91a1d2a4d0e98b8d21de6cfd9a9
Autor:
Agnieszka G. Lipska, Adam K. Sieradzan, Cezary Czaplewski, Andrea D. Lipińska, Krzysztof M. Ocetkiewicz, Jerzy Proficz, Paweł Czarnul, Henryk Krawczyk, Adam Liwo
Publikováno v:
Journal of Computational Chemistry. 44:1470-1483
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::66c15ecbeffdcbed6a7c8c8e94a38d33
https://doi.org/10.1002/jcc.27087
https://doi.org/10.1002/jcc.27087
Publikováno v:
Molecules, Vol 27, Iss 7, p 2080 (2022)
The SARS-CoV-2 virus, commonly known as COVID-19, first occurred in December 2019 in Wuhan, Hubei Province, China. Since then, it has become a tremendous threat to human health. With a pandemic threat, it is in the significant interest of the scienti
Externí odkaz:
https://doaj.org/article/10b01cf6ead84042ac918cd0e249c191
Autor:
Chen Keasar, Liam J. McGuffin, Björn Wallner, Gaurav Chopra, Badri Adhikari, Debswapna Bhattacharya, Lauren Blake, Leandro Oliveira Bortot, Renzhi Cao, B. K. Dhanasekaran, Itzhel Dimas, Rodrigo Antonio Faccioli, Eshel Faraggi, Robert Ganzynkowicz, Sambit Ghosh, Soma Ghosh, Artur Giełdoń, Lukasz Golon, Yi He, Lim Heo, Jie Hou, Main Khan, Firas Khatib, George A. Khoury, Chris Kieslich, David E. Kim, Pawel Krupa, Gyu Rie Lee, Hongbo Li, Jilong Li, Agnieszka Lipska, Adam Liwo, Ali Hassan A. Maghrabi, Milot Mirdita, Shokoufeh Mirzaei, Magdalena A. Mozolewska, Melis Onel, Sergey Ovchinnikov, Anand Shah, Utkarsh Shah, Tomer Sidi, Adam K. Sieradzan, Magdalena Ślusarz, Rafal Ślusarz, James Smadbeck, Phanourios Tamamis, Nicholas Trieber, Tomasz Wirecki, Yanping Yin, Yang Zhang, Jaume Bacardit, Maciej Baranowski, Nicholas Chapman, Seth Cooper, Alexandre Defelicibus, Jeff Flatten, Brian Koepnick, Zoran Popović, Bartlomiej Zaborowski, David Baker, Jianlin Cheng, Cezary Czaplewski, Alexandre Cláudio Botazzo Delbem, Christodoulos Floudas, Andrzej Kloczkowski, Stanislaw Ołdziej, Michael Levitt, Harold Scheraga, Chaok Seok, Johannes Söding, Saraswathi Vishveshwara, Dong Xu, Foldit Players consortium, Silvia N. Crivelli
Publikováno v:
Scientific Reports, Vol 8, Iss 1, Pp 1-18 (2018)
Abstract Every two years groups worldwide participate in the Critical Assessment of Protein Structure Prediction (CASP) experiment to blindly test the strengths and weaknesses of their computational methods. CASP has significantly advanced the field
Externí odkaz:
https://doaj.org/article/b0b847aec1154062a3c86bac14d94e55
Autor:
Adam Liwo, Cezary Czaplewski, Adam K. Sieradzan, Agnieszka G. Lipska, Sergey A. Samsonov, Rajesh K. Murarka
Publikováno v:
Biomolecules, Vol 11, Iss 9, p 1347 (2021)
Molecular dynamics with coarse-grained models is nowadays extensively used to simulate biomolecular systems at large time and size scales, compared to those accessible to all-atom molecular dynamics. In this review article, we describe the physical b
Externí odkaz:
https://doaj.org/article/e7ff07350cd848e6afbc2b062b474009
Autor:
Emilia A. Lubecka, Adam Liwo
Publikováno v:
Journal of Computational Chemistry. 43:2047-2059
The ESCASA algorithm for analytical estimation of proton positions from coarse-grained geometry developed in our recent work has been implemented in modeling protein structures with the highly coarse-grained UNRES model of polypeptide chains (two sit
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::322976e2f33bb64a00e370f336565b0a
https://doi.org/10.1002/jcc.27003
https://doi.org/10.1002/jcc.27003