We present SEEKR2
(simulation-enabled estimation of kinetic rates
version 2)—the latest iteration in the family of SEEKR programs
for using multiscale simulation methods to computationally estimate
the kinetics and thermodynamics of molecular processes, in particular,
ligand-receptor binding. SEEKR2 generates equivalent, or improved,
results compared to the earlier versions of SEEKR but with significant
increases in speed and capabilities. SEEKR2 has also been built with
greater ease of usability and with extensible features to enable future
expansions of the method. Now, in addition to supporting simulations
using NAMD, calculations may be run with the fast and extensible OpenMM
simulation engine. The Brownian dynamics portion of the calculation
has also been upgraded to Browndye 2. Furthermore, this version of
SEEKR supports hydrogen mass repartitioning, which significantly reduces
computational cost, while showing little, if any, loss of accuracy
in the predicted kinetics.
We present SEEKR2 (Simulation-Enabled Estimation of Kinetic Rates version 2) – the latest iteration in the family of SEEKR programs for using multiscale simulation methods to computationally estimate the kinetics and thermodynamics of molecular processes, in particular, ligand-receptor binding. SEEKR2 generates equivalent, or improved, results compared to the earlier versions of SEEKR, but with significant increases in speed and capabilities. SEEKR2 has also been built with greater ease of usability with extensible features to enable future expansions of the method. Now, in addition to supporting simulations using NAMD, calculations may be run with the fast and extensible OpenMM simulation engine. The Brownian dynamics portion of the calculation has also been upgraded to Browndye 2. In addition, this version of SEEKR supports hydrogen mass repartitioning to significantly reduce computational cost.
We present SEEKR2 (Simulation-Enabled Estimation of Kinetic Rates Version 2) -the latest iteration in the family of SEEKR programs for using multiscale simulation methods to computationally estimate the kinetics and thermodynamics of molecular processes, in particular, ligand-receptor binding. SEEKR2 generates equivalent, or improved, results compared to the earlier versions of SEEKR, but with significant increases in speed and capabilities. SEEKR2 has also been built with greater ease of usability with extensible features to enable future expansions of the method. Now, in addition to supporting simulations using NAMD, calculations may be run
We present SEEKR2 (Simulation-Enabled Estimation of Kinetic Rates Version 2) – the latest iteration in the family of SEEKR programs for using multiscale simulation methods to computationally estimate the kinetics and thermodynamics of molecular processes, in particular, ligand-receptor binding. SEEKR2 generates equivalent, or improved, results compared to the earlier versions of SEEKR, but with significant increases in speed and capabilities. SEEKR2 has also been built with greater ease of usability with extensible features to enable future expansions of the method. Now, in addition to supporting simulations using NAMD, calculations may be run with the fast and extensible OpenMM simulation engine. The Brownian dynamics portion of the calculation has also been upgraded to Browndye 2.
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