Zobrazeno 1 - 10
of 20
pro vyhledávání: '"Nathan R. Kern"'
Publikováno v:
Nature Communications, Vol 15, Iss 1, Pp 1-14 (2024)
Abstract Atomic-scale molecular modeling and simulation are powerful tools for computational biology. However, constructing models with large, densely packed molecules, non-water solvents, or with combinations of multiple biomembranes, polymers, and
Externí odkaz:
https://doaj.org/article/57575d3b941347678698a4b810cb92b6
Autor:
Sang-Jun Park, Jumin Lee, Yeol Kyo Choi, Seonghoon Kim, Wonpil Im, Nathan R. Kern, Soohyung Park
Publikováno v:
J Chem Theory Comput
Molecular modeling and simulations are invaluable tools for polymer science and engineering, which predict physicochemical properties of polymers and provide molecular-level insight into the underlying mechanisms. However, building realistic polymer
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::1e3dabd94188303394b55651a2d09283
https://doi.org/10.1021/acs.jctc.1c00169
https://doi.org/10.1021/acs.jctc.1c00169
Autor:
Yeol Kyo Choi, Nathan R. Kern, Seonghan Kim, Krishan Kanhaiya, Yaser Afshar, Sun Hee Jeon, Sunhwan Jo, Bernard R. Brooks, Jumin Lee, Ellad B. Tadmor, Hendrik Heinz, Wonpil Im
Publikováno v:
J Chem Theory Comput
Molecular modeling and simulation are invaluable tools for nanoscience that predict mechanical, physicochemical, and thermodynamic properties of nanomaterials and provide molecular-level insight into underlying mechanisms. However, building nanomater
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2396f254a26019ebe0d76f990fca2959
https://pubmed.ncbi.nlm.nih.gov/34871001
https://pubmed.ncbi.nlm.nih.gov/34871001
Publikováno v:
Biophysical Journal. 121:273a-274a
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::d2fad9f5aae38ea5b4cbda09d149f5b0
https://doi.org/10.1016/j.bpj.2021.11.1373
https://doi.org/10.1016/j.bpj.2021.11.1373
Autor:
InSuk Joung, Nathan R. Kern, Jooyoung Lee, Hui Sun Lee, Sunhwan Jo, Sang-Jun Park, Jumin Lee, Wonpil Im, Yifei Qi, Keehyung Joo
Publikováno v:
Glycobiology. 29:320-331
Characterizing glycans and glycoconjugates in the context of three-dimensional structures is important in understanding their biological roles and developing efficient therapeutic agents. Computational modeling and molecular simulation have become an
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::8bffb25651db8af81fe0b8a4c6b164bf
https://doi.org/10.1093/glycob/cwz003
https://doi.org/10.1093/glycob/cwz003
Autor:
Wonpil Im, Han Zhang, Seonghoon Kim, Hiraku Oshima, Wei Jiang, Yuji Sugita, Suyong Re, Jumin Lee, Benoît Roux, Nathan R. Kern
Publikováno v:
J Chem Theory Comput
Alchemical free energy simulations have long been utilized to predict free energy changes for binding affinity and solubility of small molecules. However, while the theoretical foundation of these methods is well established, seamlessly handling many
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::6121f36ee573f1114356e573bc6f90ba
https://pubmed.ncbi.nlm.nih.gov/33112150
https://pubmed.ncbi.nlm.nih.gov/33112150
Publikováno v:
The Journal of chemical physics. 153(3)
As part of our ongoing efforts to support diverse force fields and simulation programs in CHARMM-GUI, this work presents the development of FF-Converter to prepare Amber simulation inputs with various Amber force fields within the current CHARMM-GUI
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::70664e8d78876857374f304e2e2424ce
https://pubmed.ncbi.nlm.nih.gov/32716185
https://pubmed.ncbi.nlm.nih.gov/32716185
Autor:
Sang-Jun Park, Tristan I. Croll, Wonpil Im, Chaok Seok, Yeol Kyo Choi, Maham Tanveer, Hyeonuk Woo, Yiwei Cao, Min Sun Yeom, Jumin Lee, Taeyong Park, Nathan R. Kern
Publikováno v:
The Journal of Physical Chemistry. B
The Journal of Physical Chemistry B
The Journal of Physical Chemistry B
This technical study describes all-atom modeling and simulation of a fully glycosylated full-length SARS-CoV-2 spike (S) protein in a viral membrane. First, starting from PDB: 6VSB and 6VXX, full-length S protein structures were modeled using templat
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e9450446f39aa631fab9ac0b835126a3
http://europepmc.org/articles/PMC7341691
http://europepmc.org/articles/PMC7341691
Autor:
Yiwei Cao, Sang-Jun Park, Chaok Seok, Yeol Kyo Choi, Wonpil Im, Hyeonuk Woo, Maham Tanveer, Tristan I. Croll, Min Sun Yeom, Jumin Lee, Nathan R. Kern, Taeyong Park
This technical study describes all-atom modeling and simulation of a fully-glycosylated full-length SARS-CoV-2 spike (S) protein in a viral membrane. First, starting from PDB:6VSB and 6VXX, full-length S protein structures were modeled using template
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::2d5cfbbfb4da26b88d7911d9bad29186
https://doi.org/10.1101/2020.05.20.103325
https://doi.org/10.1101/2020.05.20.103325
Publikováno v:
J Phys Chem B
Nicotinic acetylcholine receptor (nAChR) participates in diverse biological processes, e.g., mood, learning, and addiction. Glycosylphosphatidylinositol (GPI)-linked lynx1 is an allosteric modulator of nAChR function, including shifts in agonist sens
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ca117d82d77ebeba35adbf0fdb1b662a
https://europepmc.org/articles/PMC7820712/
https://europepmc.org/articles/PMC7820712/