Zobrazeno 1 - 10
of 83
pro vyhledávání: '"Christopher I. Bayly"'
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:
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:
David F. Hahn, Christopher I. Bayly, Melissa L Boby, Hannah E. Bruce Macdonald, John D. Chodera, Vytautas Gapsys, Antonia S. J. S. Mey, David L. Mobley, Laura Perez Benito, Christina E. M. Schindler, Gary Tresadern, Gregory L. Warren
Publikováno v:
Living Journal of Computational Molecular Science. 4
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
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
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
Autor:
Daniel G. A. Smith, John D. Chodera, David L. Mobley, Josh Fass, Lee-Ping Wang, Christopher I. Bayly, Chaya D. Stern
Accurate molecular mechanics force fields for small molecules are essential for predicting protein-ligand binding affinities in drug discovery and understanding the biophysics of biomolecular systems. Torsion potentials derived from quantum chemical
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::1792f1f58a661051542d40894d7e0602
https://doi.org/10.1101/2020.08.27.270934
https://doi.org/10.1101/2020.08.27.270934
Autor:
Paul S. Nerenberg, Michael K. Gilson, Hyesu Jang, Michael Schauperl, Christopher I. Bayly, David L. Mobley, Lee-Ping Wang
Publikováno v:
Commun Chem
Communications chemistry, vol 3, iss 1
Communications Chemistry, Vol 3, Iss 1, Pp 1-11 (2020)
Communications chemistry, vol 3, iss 1
Communications Chemistry, Vol 3, Iss 1, Pp 1-11 (2020)
The restrained electrostatic potential (RESP) approach is a highly regarded and widely used method of assigning partial charges to molecules for simulations. RESP uses a quantum-mechanical method that yields fortuitous overpolarization and thereby ac
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::1e5cce2b27246bf8a5e4790733b0480e
https://europepmc.org/articles/PMC8204736/
https://europepmc.org/articles/PMC8204736/
Autor:
Paul S. Nerenberg, Michael Schauperl, Hyesu Jang, Michael K. Gilson, David L. Mobley, Lee-Ping Wang, Christopher I. Bayly
Many molecular simulation force fields represent the charge distributions of molecules with atom-centered partial charges, so simulations with these force fields require that partial charges be assigned to the molecules of interest. The restrained el
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::32752a9b80bb6bfb86d0ec0960860370
https://doi.org/10.26434/chemrxiv.10072799
https://doi.org/10.26434/chemrxiv.10072799