Zobrazeno 1 - 10
of 13
pro vyhledávání: '"Josh Fass"'
Autor:
Josh Fass, David A. Sivak, Gavin E. Crooks, Kyle A. Beauchamp, Benedict Leimkuhler, John D. Chodera
Publikováno v:
Entropy, Vol 20, Iss 5, p 318 (2018)
While Langevin integrators are popular in the study of equilibrium properties of complex systems, it is challenging to estimate the timestep-induced discretization error: the degree to which the sampled phase-space or configuration-space probability
Externí odkaz:
https://doaj.org/article/b60a535852db43bc8f751bb43eb0c280
Autor:
Yuanqing Wang, Josh Fass, Benjamin Kaminow, John E. Herr, Dominic Rufa, Ivy Zhang, Iván Pulido, Mike Henry, Hannah E. Bruce Macdonald, Kenichiro Takaba, John D. Chodera
Publikováno v:
Chemical Science. 13:12016-12033
Molecular mechanics (MM) potentials have long been a workhorse of computational chemistry. Leveraging accuracy and speed, these functional forms find use in a wide variety of applications in biomolecular modeling and drug discovery, from rapid virtua
Publikováno v:
Chemical Science. 12:11364-11381
The computation of tautomer ratios of druglike molecules is enormously important in computer-aided drug discovery, as over a quarter of all approved drugs can populate multiple tautomeric species in solution. Unfortunately, accurate calculations of a
Alchemical free energy calculations are an important tool in the computational chemistry toolbox, enabling the efficient calculation of quantities critical for drug discovery such as ligand binding affinities, selectivities, and partition coefficient
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::f8228486fb59aba58c1058e8f82d83c9
https://doi.org/10.1101/2021.08.24.457513
https://doi.org/10.1101/2021.08.24.457513
Autor:
Owen C. Madin, Simon Boothroyd, Richard A. Messerly, Josh Fass, John D. Chodera, Michael R. Shirts
Publikováno v:
J Chem Inf Model
A high level of physical detail in a molecular model improves its ability to perform high accuracy simulations, but can also significantly affect its complexity and computational cost. In some situations, it is worthwhile to add additional complexity
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::5d193db24384ebd174a089ce62050c68
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:
Hannah E. Bruce Macdonald, Olexandr Isayev, Patrick B. Grinaway, John D. Chodera, Dominic A. Rufa, Marcus Wieder, Josh Fass, Adrian E. Roitberg
Alchemical free energy methods with molecular mechanics (MM) force fields are now widely used in the prioritization of small molecules for synthesis in structure-enabled drug discovery projects because of their ability to deliver 1–2 kcal mol−1ac
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::244c97aa0e9637e58ac600a5e6cca883
https://doi.org/10.1101/2020.07.29.227959
https://doi.org/10.1101/2020.07.29.227959
Autor:
Ariën S. Rustenburg, Nathan M. Lim, David L. Mobley, John D. Chodera, Samuel C. Gill, Josh Fass, Gregory A. Ross, Patrick B. Grinaway
Publikováno v:
The Journal of Physical Chemistry B. 122:5579-5598
Accurately predicting protein-ligand binding affinities and binding modes is a major goal in computational chemistry, but even the prediction of ligand binding modes in proteins poses major challenges. Here, we focus on solving the binding mode predi
Autor:
Michael R. Shirts, Christopher I. Bayly, David L. Mobley, Josh Fass, Michael K. Gilson, Camila Zanette, Caitlin C. Bannan, John D. Chodera
Publikováno v:
Journal of chemical theory and computation, vol 15, iss 1
Molecular mechanics force fields define how the energy and forces of a molecular system are computed from its atomic positions, and enable the study of such systems through computational methods like molecular dynamics and Monte Carlo simulations. De
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a4166fe90516fec502c75d8543a7471e
https://doi.org/10.26434/chemrxiv.6230627.v3
https://doi.org/10.26434/chemrxiv.6230627.v3
Publikováno v:
The journal of physical chemistry. B. 122(21)
Biomolecular simulations are typically performed in an aqueous environment where the number of ions remains fixed for the duration of the simulation, generally with either a minimally neutralizing ion environment or a number of salt pairs intended to