Zobrazeno 1 - 10
of 60
pro vyhledávání: '"Jaewoon Jung"'
Publikováno v:
Nature Communications, Vol 15, Iss 1, Pp 1-14 (2024)
Abstract Residue-level coarse-grained (CG) molecular dynamics (MD) simulation is widely used to investigate slow biological processes that involve multiple proteins, nucleic acids, and their complexes. Biomolecules in a large simulation system are di
Externí odkaz:
https://doaj.org/article/f0a26f3282704ae5b3368a20231c155a
Publikováno v:
PLoS Computational Biology, Vol 18, Iss 4, p e1009578 (2022)
Residue-level coarse-grained (CG) models have become one of the most popular tools in biomolecular simulations in the trade-off between modeling accuracy and computational efficiency. To investigate large-scale biological phenomena in molecular dynam
Externí odkaz:
https://doaj.org/article/a853c17c404e4022af5f41aa197f3225
Publikováno v:
eLife, Vol 11 (2022)
Spike (S) protein is the primary antigenic target for neutralization and vaccine development for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It decorates the virus surface and undergoes large motions of its receptor binding doma
Externí odkaz:
https://doaj.org/article/e6d2fba80aa44428895594606307f61d
Autor:
Isseki Yu, Takaharu Mori, Tadashi Ando, Ryuhei Harada, Jaewoon Jung, Yuji Sugita, Michael Feig
Publikováno v:
eLife, Vol 5 (2016)
Biological macromolecules function in highly crowded cellular environments. The structure and dynamics of proteins and nucleic acids are well characterized in vitro, but in vivo crowding effects remain unclear. Using molecular dynamics simulations of
Externí odkaz:
https://doaj.org/article/98673b139fe9452fb8fdfd2b5b873997
Publikováno v:
Biophysical Reviews. 14:1503-1512
Multistate Bennett acceptance ratio (MBAR) works as a method to analyze molecular dynamics (MD) simulation data after the simulations have been finished. It is widely used to estimate free-energy changes between different states and averaged properti
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::dc552ef9900ed27046496b0d6206861a
https://doi.org/10.1007/s12551-022-01030-9
https://doi.org/10.1007/s12551-022-01030-9
Publikováno v:
Journal of Computational Chemistry.
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::da515ae4a1385746fa9537958f01296c
https://doi.org/10.1002/jcc.27124
https://doi.org/10.1002/jcc.27124
Publikováno v:
Journal of Chemical Theory and Computation. 17:5312-5321
In recent years, molecular dynamics (MD) simulations with larger time steps have been performed with the hydrogen-mass-repartitioning (HMR) scheme, where the mass of each hydrogen atom is increased to reduce high-frequency motion while the mass of a
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::08eace5263c9a54cb49e02454ba4c502
https://doi.org/10.1021/acs.jctc.1c00185
https://doi.org/10.1021/acs.jctc.1c00185
Publikováno v:
Seibutsu Butsuri. 62:298-300
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::8e421eb3a76e97de0efe807fc77caeac
https://doi.org/10.2142/biophys.62.298
https://doi.org/10.2142/biophys.62.298
Elucidation of interactions regulating conformational stability and dynamics of SARS-CoV-2 S-protein
Publikováno v:
Biophysical Journal
The ongoing COVID-19 pandemic caused by the new coronavirus, SARS-CoV-2, calls for urgent developments of vaccines and antiviral drugs. The spike protein of SARS-CoV-2 (S-protein), which consists of trimeric polypeptide chains with glycosylated resid
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::34b5582260b796744a7e339f8da41117
https://doi.org/10.1016/j.bpj.2021.01.012
https://doi.org/10.1016/j.bpj.2021.01.012
