Zobrazeno 1 - 10
of 20
pro vyhledávání: '"Victoria T. Lim"'
Publikováno v:
F1000Research, Vol 9 (2020)
Background: Force fields are used in a wide variety of contexts for classical molecular simulation, including studies on protein-ligand binding, membrane permeation, and thermophysical property prediction. The quality of these studies relies on the q
Externí odkaz:
https://doaj.org/article/80288ae17c064e61a5e9ae1f977d4894
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/
Publikováno v:
Journal of General Physiology, vol 153, iss 9
Voltage-gated sodium, potassium, and calcium channels consist of four voltage-sensing domains (VSDs) that surround a central pore domain and transition from a down state to an up state in response to membrane depolarization. While many types of drugs
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f62fc88126b91a869175c473bb82a716
https://escholarship.org/uc/item/94w0n91k
https://escholarship.org/uc/item/94w0n91k
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
Autor:
John D. Chodera, Victoria T. Lim, Caitlin C. Bannan, Andrea Rizzi, Kyle A. Beauchamp, Christopher I. Bayly, Nathan M. Lim, Michael R. Shirts, Peter Eastman, David L. Mobley, David R. Slochower, Michael K. Gilson
Publikováno v:
Journal of chemical theory and computation, vol 14, iss 11
Traditional approaches to specifying a molecular mechanics force field encode all the information needed to assign force field parameters to a given molecule into a discrete set of atom types. This is equivalent to a representation consisting of a mo
Publikováno v:
The Journal of membrane biology, vol 254, iss 1
J Membr Biol
J Membr Biol
The voltage-gated proton channel Hv1 mediates efflux of protons from the cell. Hv1 integrally contributes to various physiological processes including pH homeostasis and the respiratory burst of phagocytes. Inhibition of Hv1 may provide therapeutic a
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::bc8ac1af5f05ca879bda6117d865ef07
https://escholarship.org/uc/item/93x9v1db
https://escholarship.org/uc/item/93x9v1db
This provides Supporting Information for our work, "Benchmark assessment of molecular geometries and energies from small molecule force fields", in the form of additional plots, statistics, and analysis. Supporting datasets are also available at DOI1
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::82817b7dde348509dba498c3ff117556
Publikováno v:
J Comput Aided Mol Des
Journal of computer-aided molecular design, vol 35, iss 3
Journal of computer-aided molecular design, vol 35, iss 3
Many molecular simulation methods use force fields to help model and simulate molecules and their behavior in various environments. Force fields are sets of functions and parameters used to calculate the potential energy of a chemical system as a fun
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::067ebdfd495ae23beda15b8a8b0a52ab
https://doi.org/10.26434/chemrxiv.12846602.v1
https://doi.org/10.26434/chemrxiv.12846602.v1
Many molecular simulation methods use force fields to help model and simulate molecules and their behavior in various environments. Force fields are sets of functions and parameters used to calculate the potential energy of a chemical system as a fun
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::d69a25839928525e3d4f71b3e1d2eabd
https://doi.org/10.26434/chemrxiv.12846602
https://doi.org/10.26434/chemrxiv.12846602
Autor:
Linnea S. Axelsson, Urska Rovsnik, Rebecca J. Howard, Victoria T. Lim, Björn O. Forsberg, Christian Blau, Marta Carroni, Erik Lindahl, Yuxuan Zhuang
Ligand-gated ion channels are critical mediators of electrochemical signal transduction across evolution. Biophysical and pharmacological development in this family relies on high-quality structural data in multiple, subtly distinct functional states
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::864880c6bf2b05da2f3df0aca12fc418
https://doi.org/10.1101/2020.06.19.161356
https://doi.org/10.1101/2020.06.19.161356