Sentence examples for molecular simulation package from inspiring English sources

All the descriptors were calculated using Discovery Studio molecular simulation package (version 2.5) [38].

The multi-purpose simulation code of the molecular simulation package was used for all simulations [28].

The principal component analysis was performed using the MOE molecular simulation package.

The SMILES of the 7385 structures in the data set were converted into 3-D structures and optimized in Discovery Studio 2.5 molecular simulation package (DS 2.5) [16].

The twelve fractional descriptors for water accessible surface and van der Waals surface were calculated using MOE molecular simulation package [29].

Here, 68 molecules were eliminated because some molecular descriptors of them could not be successfully generated by Molecular Operating Environment MOEE) 2009 molecular simulation package [17], and 3 molecules with pLD50 values higher than 7.0 or lower than 0, distantly distributed from the other data, were removed.

Moreover, two popular molecular simulation packages, including Discovery Studio (version 2.5) [16] and SYBYL-X (version 1.3) [17], were used to perceive the molecules in the second data set.

We note that analysis tools within molecular simulation packages that calculate SASA, such as the g_sas module in GROMACS, often base definitions of polar and non-polar surface areas on atomic partial charges taken from the molecular potential being used.

We present a comprehensive molecular simulation program package, the Peking University Drug Design System (PKUDDS), which runs on personal computers.

The molecular dynamics simulation package, MATERIALS EXPLORER [17], was used in the present work.

The MD simulations described in this work were performed using the classical molecular dynamics simulation package LAMMPS [20].