Zobrazeno 1 - 9
of 9
pro vyhledávání: '"Chaya D Stern"'
Autor:
Peter Eastman, Jason Swails, John D Chodera, Robert T McGibbon, Yutong Zhao, Kyle A Beauchamp, Lee-Ping Wang, Andrew C Simmonett, Matthew P Harrigan, Chaya D Stern, Rafal P Wiewiora, Bernard R Brooks, Vijay S Pande
Publikováno v:
PLoS Computational Biology, Vol 13, Iss 7, p e1005659 (2017)
OpenMM is a molecular dynamics simulation toolkit with a unique focus on extensibility. It allows users to easily add new features, including forces with novel functional forms, new integration algorithms, and new simulation protocols. Those features
Externí odkaz:
https://doaj.org/article/a3c536fb0ab14c8bbc0cb33e5bac84f0
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
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:
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
The parameterization of torsional / dihedral angle potential energy terms is a crucial part of developing molecular mechanics force fields.Quantum mechanical (QM) methods are often used to provide samples of the potential energy surface (PES) for fit
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::b60cf2d2aad225891aaba6e1ef27f39a
https://doi.org/10.26434/chemrxiv.12044673.v1
https://doi.org/10.26434/chemrxiv.12044673.v1
Publikováno v:
The Journal of chemical physics, vol 152, iss 24
J Chem Phys
J Chem Phys
The parameterization of torsional/dihedral angle potential energy terms is a crucial part of developing molecular mechanics force fields. Quantum mechanical (QM) methods are often used to provide samples of the potential energy surface (PES) for fitt
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::73f01a4da4b1764a451e4ba8917b27ae
https://doi.org/10.1063/5.0009232
https://doi.org/10.1063/5.0009232
Autor:
Andrew C. Simmonett, Bernard R. Brooks, Jason M. Swails, Rafal P. Wiewiora, Robert T. McGibbon, Peter Eastman, John D. Chodera, Kyle A. Beauchamp, Vijay S. Pande, Lee-Ping Wang, Chaya D. Stern, Yutong Zhao, Matthew P. Harrigan
Publikováno v:
PLoS Computational Biology, Vol 13, Iss 7, p e1005659 (2017)
PLoS computational biology, vol 13, iss 7
PLoS Computational Biology
PLoS computational biology, vol 13, iss 7
PLoS Computational Biology
OpenMM is a molecular dynamics simulation toolkit with a unique focus on extensibility. It allows users to easily add new features, including forces with novel functional forms, new integration algorithms, and new simulation protocols. Those features
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::9c6af50dcc8d8d8e0cc990eec49d774a
https://doi.org/10.1101/091801
https://doi.org/10.1101/091801
Autor:
Adina Heinberg, Laura A. Kirkman, Chaya D. Stern, Edwin Siu, Kirk W. Deitsch, Michael T. Ferdig, Elizabeth A. Lawrence
Publikováno v:
Molecular Microbiology. 88:702-712
Summary Resistance to antimalarials targeting the folate pathway is widespread. GTP-cyclohydrolase (gch1), the first enzyme in this pathway, exhibits extensive copy number variation (CN) in parasite isolates from areas with a history of longstanding
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::760c86783f23df633b30ecb91dab0ec1
https://doi.org/10.1111/mmi.12162
https://doi.org/10.1111/mmi.12162
Autor:
Chaya D. Stern, Jose Manuel Perez-Aguilar, Harel Weinstein, Scott C. Blanchard, John D. Chodera
Publikováno v:
Biophysical Journal. 110(3):324a-325a
GPCRs transduce extracellular signals to intracellular downstream pathway via their ability to dynamically change their orientation to different functional conformations. While kinetic experiments such as correlation spectroscopy or Forster resonance
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::7aa50c8e864a37eb85ebf81ea841d7ab