Zobrazeno 1 - 10
of 22
pro vyhledávání: '"Trevor Gokey"'
Publikováno v:
PLoS ONE, Vol 13, Iss 9, p e0203889 (2018)
The active form of vitamin B6, pyridoxal 5'-phosphate (PLP), plays an essential role in the catalytic mechanism of various proteins, including human glutamate-oxaloacetate transaminase (hGOT1), an important enzyme in amino acid metabolism. A recent m
Externí odkaz:
https://doaj.org/article/0be0fbcbec524c219e1e6950594b396b
Autor:
Joshua T. Horton, Simon Boothroyd, Jeffrey Wagner, Joshua A. Mitchell, Trevor Gokey, David L. Dotson, Pavan Kumar Behara, Venkata Krishnan Ramaswamy, Mark Mackey, John D. Chodera, Jamshed Anwar, David L. Mobley, Daniel J. Cole
Publikováno v:
Journal of Chemical Information and Modeling. 62:5622-5633
The development of accurate transferable force fields is key to realizing the full potential of atomistic modeling in the study of biological processes such as protein-ligand binding for drug discovery. State-of-the-art transferable force fields, suc
Autor:
Simon Boothroyd, Pavan Kumar Behara, Owen C. Madin, David F. Hahn, Hyesu Jang, Vytautas Gapsys, Jeffrey R. Wagner, Joshua T. Horton, David L. Dotson, Matthew W. Thompson, Jessica Maat, Trevor Gokey, Lee-Ping Wang, Daniel J. Cole, Michael K. Gilson, John D. Chodera, Christopher I. Bayly, Michael R. Shirts, David L. Mobley
Publikováno v:
Journal of chemical theory and computation, vol 19, iss 11
We introduce the Open Force Field (OpenFF) 2.0.0 small molecule force field for drug-like molecules, code-named Sage, which builds upon our previous iteration, Parsley. OpenFF force fields are based on direct chemical perception, which generalizes ea
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::fb71789c7555db802bd690b7ec3bb1ad
https://escholarship.org/uc/item/35b7v1pz
https://escholarship.org/uc/item/35b7v1pz
Autor:
Simon Boothroyd, Pavan Kumar Behara, Owen Madin, David Hahn, Hyesu Jang, Vytautas Gapsys, Jeffrey Wagner, Joshua Horton, David Dotson, Matthew Thompson, Jessica Maat, Trevor Gokey, Lee-Ping Wang, Daniel Cole, Michael Gilson, John Chodera, Christopher Bayly, Michael Shirts, David Mobley
We introduce the Open Force Field (OpenFF) 2.0.0 small molecule force field for drug-like molecules, code-named Sage, which builds upon our previous iteration, Parsley. OpenFF force fields are based on direct chemical perception, which generalizes ea
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c0504fe14a152ad3e76dd45d1eae6f33
https://doi.org/10.26434/chemrxiv-2022-n2z1c
https://doi.org/10.26434/chemrxiv-2022-n2z1c
Autor:
Joshua Horton, Simon Boothroyd, Jeffrey Wagner, Joshua Mitchell, Trevor Gokey, David Dotson, Pavan Behara, Venkata Ramaswamy, Mark Mackey, John Chodera, Jamshed Anwar, David Mobley, Daniel Cole
The development of accurate transferable force fields is key to realizing the full potential of atomistic modelling in the study of biological processes such as protein--ligand binding for drug discovery. State-of-the-art transferable force fields, s
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::d15576ddddcf740df7a0345f32f55204
https://doi.org/10.26434/chemrxiv-2022-6h628
https://doi.org/10.26434/chemrxiv-2022-6h628
Autor:
Michael K. Gilson, John D. Chodera, Bryon Tjanaka, Daniel A. Smith, Caitlin C. Bannan, Hyesu Jang, Michael R. Shirts, Yudong Qiu, Chaya D. Stern, Trevor Gokey, Lee-Ping Wang, Xavier Lucas, Victoria T. Lim, Christopher I. Bayly, David F. Hahn, Simon Boothroyd, David L. Mobley, Gary Tresadern, Andrea Rizzi, Jeffrey R. Wagner
Publikováno v:
J Chem Theory Comput
We present a methodology for defining and optimizing a general force field for classical molecular simulations, and we describe its use to derive the Open Force Field 1.0.0 small-molecule force field, codenamed Parsley. Rather than using traditional
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::52338355a022b64066c79c1a5a224008
https://europepmc.org/articles/PMC8511297/
https://europepmc.org/articles/PMC8511297/
Autor:
Yudong Qiu, Daniel Smith, Simon Boothroyd, Hyesu Jang, Jeffrey Wagner, Caitlin C. Bannan, Trevor Gokey, Victoria T. Lim, Chaya Stern, Andrea Rizzi, Xavier Lucas, Bryon Tjanaka, Michael R. Shirts, Michael Gilson, John Chodera, Christopher I. Bayly, David Mobley, Lee-Ping Wang
We present a methodology for defining and optimizing a general force field for classical molecular simulations, and we describe its use to derive the Open Force Field 1.0.0 small molecule force field, code-named Parsley. Rather than traditional atom-
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2894c07fae81a3ec8972bd475567e204
https://doi.org/10.26434/chemrxiv-2021-l070l-v4
https://doi.org/10.26434/chemrxiv-2021-l070l-v4
Publikováno v:
The Journal of chemical physics. 153(15)
We consider the recently developed weighted ensemble milestoning (WEM) scheme [J. Chem. Phys. 152, 234114 (2020)], and test its capability of simulating ligand-receptor dissociation dynamics. We performed WEM simulations on the following host-guest s
Publikováno v:
Journal of Structural Biology. 202:175-181
Many bacteria require L-rhamnose as a key cell wall component. This sugar is transferred to the cell wall using an activated donor dTDP-L-rhamnose, which is produced by the dTDP-L-rhamnose biosynthetic pathway. We determined the crystal structure of
Autor:
Ten-Yang Yen, Stephanie R. Gee, Hana Martucci, Walter M. Bray, Trevor Gokey, Scott Campit, A. King Cada, Taro Amagata, Katsuhiko Minoura, Anton B. Guliaev, R. Scott Lokey
Publikováno v:
Journal of Natural Products. 80:684-691
HeLa cell-based cytological profiling (CP) was applied to an extract library of marine sediment-derived actinomycetes to discover new cytotoxic secondary metabolites. Among the hit strains, Streptomyces sp. CP26-58 was selected for further investigat