Zobrazeno 1 - 10
of 15
pro vyhledávání: '"R. Gregor Weiß"'
Autor:
Flavio C. C. Galeazzo, Marta Garcia-Gasulla, Elisabetta Boella, Josep Pocurull, Sergey Lesnik, Henrik Rusche, Simone Bnà, Matteo Cerminara, Federico Brogi, Filippo Marchetti, Daniele Gregori, R. Gregor Weiß, Andreas Ruopp
Publikováno v:
Computers, Vol 13, Iss 5, p 115 (2024)
OpenFOAM is a CFD software widely used in both industry and academia. The exaFOAM project aims at enhancing the HPC scalability of OpenFOAM, while identifying its current bottlenecks and proposing ways to overcome them. For the assessment of the soft
Externí odkaz:
https://doaj.org/article/7db566b5ac56428bbff8db0aa44afd9d
Autor:
Benjamin Ries, Karl Normak, R. Gregor Weiß, Salomé Rieder, Emília P. Barros, Candide Champion, Gerhard König, Sereina Riniker
Publikováno v:
Journal of Computer-Aided Molecular Design, 36 (2)
The calculation of relative free-energy differences between different compounds plays an important role in drug design to identify potent binders for a given protein target. Most rigorous methods based on molecular dynamics simulations estimate the f
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2007c94a11c861fe266cef717ebc375f
https://doi.org/10.1007/s10822-021-00436-z
https://doi.org/10.1007/s10822-021-00436-z
Autor:
R. Gregor Weiß, Christoph Giese, Markus Aebi, Sereina Riniker, Marie-Estelle Losfeld, Corina Mathew, Rudi Glockshuber, Chia-Wei Lin
Publikováno v:
RSC Chemical Biology. 2:917-931
A hallmark of N-linked glycosylation in the secretory compartments of eukaryotic cells is the sequential remodeling of an initially uniform oligosaccharide to a site-specific, heterogeneous ensemble of glycostructures on mature proteins. To understan
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::49c01eaebf3a3bcd085880f052f7ed94
https://doi.org/10.1039/d1cb00019e
https://doi.org/10.1039/d1cb00019e
Publikováno v:
The journal of physical chemistry. B. 125(33)
Secreted proteins of eukaryotes are decorated with branched carbohydrate oligomers called glycans. This fact is only starting to be considered for in silico investigations of protein dynamics. Using all-atom molecular dynamics (MD) simulations and Ma
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::6666efff1c7905de32b8a899d88e8a7a
https://pubmed.ncbi.nlm.nih.gov/34379416
https://pubmed.ncbi.nlm.nih.gov/34379416
Autor:
Corina, Mathew, R Gregor, Weiß, Christoph, Giese, Chia-Wei, Lin, Marie-Estelle, Losfeld, Rudi, Glockshuber, Sereina, Riniker, Markus, Aebi
Publikováno v:
Rsc Chemical Biology
A hallmark of N-linked glycosylation in the secretory compartments of eukaryotic cells is the sequential remodeling of an initially uniform oligosaccharide to a site-specific, heterogeneous ensemble of glycostructures on mature proteins. To understan
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=pmid________::fa64462e0988231d34005eae71dc10a9
https://pubmed.ncbi.nlm.nih.gov/34212152
https://pubmed.ncbi.nlm.nih.gov/34212152
Publikováno v:
The Journal of Chemical Physics, 153 (23)
Thermally driven processes of molecular systems include transitions of energy barriers on the microsecond timescales and higher. Sufficient sampling of such processes with molecular dynamics simulations is challenging and often requires accelerating
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::88d66492c8d13d1df05baac987bf56f3
https://pubmed.ncbi.nlm.nih.gov/33353335
https://pubmed.ncbi.nlm.nih.gov/33353335
Using explicit-water molecular dynamics (MD) simulations of a generic pocket-ligand model we investigate how chemical and shape anisotropy of small ligands influences the affinities, kinetic rates and pathways for their association to hydrophobic bin
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::70a7990ba369efb0bbc15b30ff54fb9d
http://arxiv.org/abs/2009.08144
http://arxiv.org/abs/2009.08144
Publikováno v:
The Journal of Chemical Physics, 154 (8)
The combination of Markov state modeling (MSM) and molecular dynamics (MD) simulations has been shown in recent years to be a valuable approach to unravel the slow processes of molecular systems with increasing complexity. While the algorithms for in
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::8425b373d9506c94f30a947190f1e553
Publikováno v:
Journal of Chemical Theory and Computation. 13:3012-3019
We investigate how to tune the rate of hydrophobic ligand-receptor association due to the role of solvent in adjustable receptor pockets by explicit-water molecular dynamics (MD) simulations. Our model considers the binding of a spherical ligand (key
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2290a3869b3178992cabe80b325c09b0
https://doi.org/10.1021/acs.jctc.7b00216
https://doi.org/10.1021/acs.jctc.7b00216
Publikováno v:
Proceedings of the National Academy of Sciences
Proceedings of the National Academy of Sciences of the United States of America, vol 116, iss 30
Proceedings of the National Academy of Sciences of the United States of America, vol 116, iss 30
Ligand-receptor binding and unbinding are fundamental biomolecular processes and particularly essential to drug efficacy. Environmental water fluctuations, however, impact the corresponding thermodynamics and kinetics and thereby challenge theoretica
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a560c0d7e7535da65ff5febb18784c8f