Zobrazeno 1 - 10
of 10
pro vyhledávání: '"Crystal N. Nguyen"'
Autor:
Takeshi Yamazaki, Tyler Luchko, Michael K. Gilson, Tom Kurtzman, Crystal N. Nguyen, Andriy Kovalenko, David A. Case
Publikováno v:
PLoS ONE
PLoS ONE, Vol 14, Iss 7, p e0219473 (2019)
PLoS ONE, Vol 14, Iss 7, p e0219473 (2019)
Computed, high-resolution, spatial distributions of solvation energy and entropy can provide detailed information about the role of water in molecular recognition. While grid inhomogeneous solvation theory (GIST) provides rigorous, detailed thermodyn
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::076bfd6a1eaeb74659f862098e8d0fc4
https://nrc-publications.canada.ca/eng/view/object/?id=6a7d0ce4-910e-45b0-bbc9-ff0069ed0281
https://nrc-publications.canada.ca/eng/view/object/?id=6a7d0ce4-910e-45b0-bbc9-ff0069ed0281
Autor:
Crystal N. Nguyen, Ross C. Walker, Tom Kurtzman, Michael K. Gilson, Romelia Salomon-Ferrer, Steven Ramsey
Publikováno v:
Journal of Computational Chemistry. 37:2029-2037
The expulsion of water from surfaces upon molecular recognition and nonspecific association makes a major contribution to the free energy changes of these processes. In order to facilitate the characterization of water structure and thermodynamics on
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d492abf22ba78a854e43a8fdf719deea
https://doi.org/10.1002/jcc.24417
https://doi.org/10.1002/jcc.24417
Autor:
Emilio Gallicchio, Peng He, Ronald M. Levy, Lauren Wickstrom, Ahmet Mentes, Nanjie Deng, Michael K. Gilson, Tom Kurtzman, Crystal N. Nguyen
Publikováno v:
Journal of Molecular Recognition. 29:10-21
Force field accuracy is still one of the "stalemates" in biomolecular modeling. Model systems with high quality experimental data are valuable instruments for the validation and improvement of effective potentials. With respect to protein-ligand bind
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::71ed7770c0eefdf6ac34294adaa3921f
https://doi.org/10.1002/jmr.2489
https://doi.org/10.1002/jmr.2489
Autor:
Marcus Fischer, Michael K. Gilson, Brian K. Shoichet, Reed M. Stein, Crystal N. Nguyen, Anthony Cruz, Trent E. Balius, Tom Kurtzman, Thomas B. Adler
Publikováno v:
Proceedings of the National Academy of Sciences. 114
Binding-site water is often displaced upon ligand recognition, but is commonly neglected in structure-based ligand discovery. Inhomogeneous solvation theory (IST) has become popular for treating this effect, but it has not been tested in controlled e
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::84945dd8e6e5e9a2d3fea3c533ebc569
https://doi.org/10.1073/pnas.1703287114
https://doi.org/10.1073/pnas.1703287114
Publikováno v:
Journal of Chemical Theory and Computation
A number of computational tools available today compute the thermodynamic properties of water at surfaces and in binding pockets by using inhomogeneous solvation theory (IST) to analyze explicit-solvent simulations. Such methods enable qualitative sp
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::5e9ff4067f1a79d1710a50ed6c905f8a
https://pubmed.ncbi.nlm.nih.gov/26636620
https://pubmed.ncbi.nlm.nih.gov/26636620
Publikováno v:
Journal of Chemical Theory and Computation
Water molecules in the active site of an enzyme occupy a complex, heterogeneous environment, and the thermodynamic properties of active-site water are functions of position. As a consequence, it is thought that an enzyme inhibitor can gain affinity b
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::9f66235559104576cb598df4f68ee485
https://pubmed.ncbi.nlm.nih.gov/25018673
https://pubmed.ncbi.nlm.nih.gov/25018673
Publikováno v:
The Journal of chemical physics. 136(18)
It has been suggested that the most-efficient pathway taken by a slowly diffusing many-body system is its geodesic path through the parts of the potential energy landscape lying below a prescribed value of the potential energy. From this perspective,
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::88a731384657ccfe3d3feb142e8b4781
https://pubmed.ncbi.nlm.nih.gov/22583297
https://pubmed.ncbi.nlm.nih.gov/22583297
Publikováno v:
The Journal of Chemical Physics. 137:044101
The displacement of perturbed water upon binding is believed to play a critical role in the thermodynamics of biomolecular recognition, but it is nontrivial to unambiguously define and answer questions about this process. We address this issue by int
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::581f1f1000f2abed13ef0cad5489f182
https://doi.org/10.1063/1.4733951
https://doi.org/10.1063/1.4733951
Autor:
Crystal N. Nguyen, Richard M. Stratt
Publikováno v:
The Journal of Chemical Physics. 133:124503
It is not obvious that many-body phenomena as collective as solute energy relaxation in liquid solution should ever have identifiable molecular mechanisms, at least not in the sense of the well-defined sequence of molecular events one often attribute
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4145d1cef62759132613b02a3edd2186
https://doi.org/10.1063/1.3481655
https://doi.org/10.1063/1.3481655