Zobrazeno 1 - 10
of 23
pro vyhledávání: '"James F. Dama"'
Autor:
John M. A. Grime, James F. Dama, Barbie K. Ganser-Pornillos, Cora L. Woodward, Grant J. Jensen, Mark Yeager, Gregory A. Voth
Publikováno v:
Nature Communications, Vol 7, Iss 1, Pp 1-11 (2016)
Significant morphological changes occur during the conversion of the immature HIV virion into a mature infectious form. Here the authors use coarse-grained molecular dynamics simulations to model HIV-1 capsid self-assembly and disassembly events that
Externí odkaz:
https://doaj.org/article/cb54a296583545b2ab2085fab3f7c41c
Publikováno v:
Journal of Chemical Theory and Computation
The protein mediated hydrolysis of nucleoside triphosphates such as ATP or GTP is one of the most important and challenging biochemical reactions in nature. The chemical environment (water structure, catalytic metal, and amino acid residues) adjacent
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::20163ece8f3a73175bc85c6733d922ab
http://europepmc.org/articles/PMC5425946
http://europepmc.org/articles/PMC5425946
Publikováno v:
Journal of Chemical Theory and Computation. 12:5157-5169
Metadynamics is an important enhanced sampling technique in molecular dynamics simulation to efficiently explore potential energy surfaces. The recently developed transition-tempered metadynamics (TTMetaD) has been proven to converge asymptotically w
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a92cc0ec218e4b8526d1692f4bb6c9b1
https://doi.org/10.1021/acs.jctc.6b00206
https://doi.org/10.1021/acs.jctc.6b00206
Publikováno v:
The Journal of chemical physics. 149(4)
Mesoscopic models are widely used to study complex organization and transport phenomena in chemical and biological systems. Defining a rigorous procedure by which a mesoscopic coarse-grained (CG) representation for a fluid can be constructed from an
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ed4d5c99c7ee2c7268a914e01a69c32a
https://pubmed.ncbi.nlm.nih.gov/30068206
https://pubmed.ncbi.nlm.nih.gov/30068206
Publikováno v:
Journal of chemical theory and computation. 14(4)
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::aca7cf1d3a9e1f50814d8be865dcc520
https://pubmed.ncbi.nlm.nih.gov/28112956
https://pubmed.ncbi.nlm.nih.gov/28112956
Publikováno v:
Journal of Chemical Theory and Computation. 11:3547-3560
The sensitivity of a coarse-grained (CG) force field to changes in the underlying fine-grained (FG) model from which it was derived provides modeling insight for improving transferability across interaction parameters, transferability across temperat
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ae70b92aa2a6afcf9258e6c2fdc5e8fe
https://doi.org/10.1021/acs.jctc.5b00180
https://doi.org/10.1021/acs.jctc.5b00180
Publikováno v:
Journal of Chemical Theory and Computation. 11:2451-2460
Creating models that are consistent with experimental data is essential in molecular modeling. This is often done by iteratively tuning the molecular force field of a simulation to match experimental data. An alternative method is to bias a simulatio
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c08ee71c49b3cd3cef155a80433cf814
https://doi.org/10.1021/acs.jctc.5b00178
https://doi.org/10.1021/acs.jctc.5b00178
Publikováno v:
Journal of Chemical Theory and Computation. 10:5265-5275
The increasing interest in the modeling of complex macromolecular systems in recent years has spurred the development of numerous coarse-graining (CG) techniques. However, many of the CG models are constructed assuming that all details beneath the re
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::5a5c558b60e18c931001a653446738a5
https://doi.org/10.1021/ct500834t
https://doi.org/10.1021/ct500834t
Publikováno v:
Journal of chemical theory and computation. 13(3)
When viewed through a coarse-grained lens, important molecular and biophysical systems can appear to undergo discrete, switch-like state changes in addition to more continuous configurational motions. One of our recent papers described a theory for b
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e21a151b2ed7c378232f7af39ae469e5
https://pubmed.ncbi.nlm.nih.gov/29509418
https://pubmed.ncbi.nlm.nih.gov/29509418
Autor:
Aaron R. Dinner, Benoiît Roux, Gregory A. Voth, Jonathan Weare, Martin McCullagh, James F. Dama, Anton V. Sinitskiy
Publikováno v:
Journal of Chemical Theory and Computation. 9:2466-2480
Coarse-grained (CG) models provide a computationally efficient means to study biomolecular and other soft matter processes involving large numbers of atoms correlated over distance scales of many covalent bond lengths and long time scales. Variationa
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::307b14174a5864bda704235b651c605e
https://doi.org/10.1021/ct4000444
https://doi.org/10.1021/ct4000444