Sentence examples for binding simulations were performed from inspiring English sources

An unbound conformation was defined by the fraction of native contact Qb = 0 and a mass-center distance between the two proteins ΔR>45 Å. Subsequently, 400 binding simulations were performed starting from 400 unbound structures.

To predict the binding mode of the complex, molecular docking simulations were performed with AutoDock 4.0[32], [33] docking tool.

MD simulations were performed to approximate binding affinities for both d- and l-nucleosides, as well as nucleoside analogues bound to selected dCK variants.

Multiscale simulation studies using Brownian dynamics and molecular-dynamics simulations were performed to provide the binding process on multiple length- and timescales.

Theoretical simulations were performed using density-functional tight-binding theory.

Over the past few years, numerous docking studies and molecular dynamic simulations were performed in an attempt to elucidate the binding modes of tyrosinase inhibitors.

The docking simulations were performed on a model of TrkA ligand binding domain obtained deleting the NGF from the NGF-TrkA co-crystal (PDBcode: 1WWW).

As a test of the utility of the methods in an evolutionary context, simulations were performed under negative selection for protein folding and binding.

Simulations were performed using PNNL Institutional Computing Resources.

Simulations were performed using Matlab.

All simulations were performed using the Neuron Simulation Environment58.