Zobrazeno 1 - 10
of 18
pro vyhledávání: '"John Chodera"'
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
Publikováno v:
J Chem Theory Comput
Developing accurate classical force field representations of molecules is key to realizing the full potential of molecular simulations, both as a powerful route to gaining fundamental insights into a broad spectrum of chemical and biological phenomen
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c219f455370d564e8c5c145433ceb238
https://europepmc.org/articles/PMC9245177/
https://europepmc.org/articles/PMC9245177/
Autor:
David Dotson, John Chodera, David Mobley, Christopher Bayly, Jessica Maat, Daniel Smith, Chaya D. Stern
Accurate small molecule force fields are crucial for predicting thermodynamic and kinetic properties of drug-like molecules in biomolecular systems. Torsion parameters, in particular, are essential for determining conformational distribution of molec
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::b1ef336f8431e154550cd868b6ec54f5
https://doi.org/10.1101/2022.01.17.476653
https://doi.org/10.1101/2022.01.17.476653
Developing a sufficiently accurate classical force field representation of molecules is key to realizing the full potential of molecular simulation as a route to gaining fundamental insight into a broad spectrum of chemical and biological phenomena.
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::aaa81008380e154f8706aedc0013919e
https://doi.org/10.26434/chemrxiv-2021-gsgr4-v2
https://doi.org/10.26434/chemrxiv-2021-gsgr4-v2
Autor:
Anthony Aimon, John Chodera, David Mobley, Frank Von Delft, Mehtap Işık, Harold Grosjean, Philip Biggin
Publikováno v:
Journal of computer-aided molecular design, vol 36, iss 4
A novel crystallographic fragment screening data set was generated and used in the SAMPL7 challenge for protein-ligands. The SAMPL challenges prospectively assess the predictive power of methods involved in computer-aided drug design. Application of
The COVID-19 pandemic is a stark reminder that a barren global antiviral pipeline has grave humanitarian consequences. Future pandemics could be prevented by accessible, easily deployable broad-spectrum oral antivirals and open knowledge bases that d
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::8b7c6e31fcc5eff3442a22094ef899e9
https://doi.org/10.33774/chemrxiv-2021-585ks-v2
https://doi.org/10.33774/chemrxiv-2021-585ks-v2
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:
Viraj Sanghvi, Aleksander Rust, Josef Leibold, Scott Lowe, Agnes Viale, John Chodera, Ronald C. Hendrickson, Elisa de Stanchina, Hans-Guido Wendel
Publikováno v:
Clinical Cancer Research. 28:PO029-PO029
NRF2 is an “undruggable” oncogenic transcription factor recurrently mutated in solid tumors such as liver and lung cancers. Our recent study demonstrates that NRF2 acts by coordinating the redox and metabolic stress responses as well as drug resi
Autor:
Frank, von Delft, Mark, Calmiano, John, Chodera, Ed, Griffen, Alpha, Lee, Nir, London, Tatiana, Matviuk, Ben, Perry, Matt, Robinson, Annette, von Delft
Publikováno v:
Nature. 594(7863)