Zobrazeno 1 - 10
of 71
pro vyhledávání: '"Li-Tien Cheng"'
Publikováno v:
Frontiers in Molecular Biosciences, Vol 5 (2018)
Predicting solvation free energies and describing the complex water behavior that plays an important role in essentially all biological processes is a major challenge from the computational standpoint. While an atomistic, explicit description of the
Externí odkaz:
https://doaj.org/article/6bf199dc52824e2da0c69084d6637790
Publikováno v:
SIAM Journal on Applied Mathematics; 2024, Vol. 84 Issue 3, pS515-S537, 23p
Autor:
ZIRUI ZHANG, RAY, LI-TIEN CHENG
Publikováno v:
SIAM Journal on Scientific Computing; 2023, Vol. 45 Issue 5, pB618-B645, 28p
Publikováno v:
J Chem Theory Comput
Journal of chemical theory and computation, vol 17, iss 4
Journal of chemical theory and computation, vol 17, iss 4
We develop a hybrid approach that combines the Monte Carlo (MC) method, a variational implicit-solvent model (VISM), and a binary level-set method for the simulation of biomolecular binding in an aqueous solvent. The solvation free energy for the bio
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c012d22ffaab6df21ea900b7d4cde152
https://doi.org/10.1021/acs.jctc.0c01109
https://doi.org/10.1021/acs.jctc.0c01109
Publikováno v:
Journal of Computational Physics. 472:111673
Coarse-grained modeling and efficient computer simulations are critical to the study of complex molecular processes with many degrees of freedom and multiple spatiotemporal scales. Variational implicit-solvent model (VISM) for biomolecular solvation
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a41cc76606f41892b24d00b15c4d090d
https://doi.org/10.1016/j.jcp.2022.111673
https://doi.org/10.1016/j.jcp.2022.111673
Publikováno v:
The Journal of chemical physics. 155(12)
Water fluctuates in a hydrophobic confinement, forming multiple dry and wet hydration states through evaporation and condensation. Transitions between such states are critical to both thermodynamics and kinetics of solute molecular processes, such as
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::08c320be2a980e39e29ee3743307be1a
https://pubmed.ncbi.nlm.nih.gov/34598586
https://pubmed.ncbi.nlm.nih.gov/34598586
Publikováno v:
Journal of Computational Physics. 374:533-549
We develop a computational model for the solvation of charged molecules in an aqueous solvent. Such solvent is modeled as an incompressible fluid, and its dynamics is described by the Stokes equations. All the surface tension force, van der Waals dis
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::ccb188507ab5822e916036282583aac6
https://doi.org/10.1016/j.jcp.2018.07.046
https://doi.org/10.1016/j.jcp.2018.07.046
Publikováno v:
Proceedings of the National Academy of Sciences
Proceedings of the National Academy of Sciences of the United States of America, vol 116, iss 30
Proceedings of the National Academy of Sciences of the United States of America, vol 116, iss 30
Ligand-receptor binding and unbinding are fundamental biomolecular processes and particularly essential to drug efficacy. Environmental water fluctuations, however, impact the corresponding thermodynamics and kinetics and thereby challenge theoretica
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a560c0d7e7535da65ff5febb18784c8f
Publikováno v:
Journal of Chemical Physics; 2016, Vol. 145 Issue 5, p054114-1-054114-11, 11p, 2 Color Photographs, 1 Diagram, 1 Chart, 5 Graphs
Publikováno v:
Journal of chemical theory and computation, vol 11, iss 2
Guo, Z; Li, B; Cheng, LT; Zhou, S; McCammon, JA; & Che, J. (2015). Identification of protein-ligand binding sites by the level-set variational implicit-solvent approach. Journal of Chemical Theory and Computation, 11(2), 753-765. doi: 10.1021/ct500867u. UC San Diego: Retrieved from: http://www.escholarship.org/uc/item/6z55f5w3
Journal of Chemical Theory and Computation
Guo, Z; Li, B; Cheng, LT; Zhou, S; McCammon, JA; & Che, J. (2015). Identification of protein-ligand binding sites by the level-set variational implicit-solvent approach. Journal of Chemical Theory and Computation, 11(2), 753-765. doi: 10.1021/ct500867u. UC San Diego: Retrieved from: http://www.escholarship.org/uc/item/6z55f5w3
Journal of Chemical Theory and Computation
© 2015 American Chemical Society. Protein-ligand binding is a key biological process at the molecular level. The identification and characterization of small-molecule binding sites on therapeutically relevant proteins have tremendous implications fo
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::83c74233ad182d77412a593ba75798ce
https://doi.org/10.1021/ct500867u
https://doi.org/10.1021/ct500867u