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An energy-minimized model of A66 was generated using SKETCHER (SYBYL8.2, Tripos) and minimized using MAXMIN2 with the MMFF94s forcefield and MMFF94 charges.

The stereochemical assignments of methylene hydrogens shown in Table 2 [see Additional files 3, 4, 5] were made based on gradient NOESY cross-peaks and were consistent with distances determined from a computational, energy-minimized model of the molecule utilizing the MMX force-field (PCModel, version 9.2; Serena Software, Bloomington, IN).

The crystal structure of hCE1 in covalent complex with cyclosarin was then used to generate an energy-minimized model of V146H/L363E hCE1.

An energy-minimized model of a complex of 12 with this enzyme is shown in Figure 3B.

The minimized models for the four states of the B-form DNA duplex with the 9-mer strand CGCCCGGCT pairing with a complementary strand 6-mer AGCCGG were solvated in a 54 Å dimension cubic box with a random distribution of 21 sodium ions and 7 chloride ions obtained through Monte Carlo optimization.

No significant differences in the secondary structure were observed among the energy-minimized models of the variants, and computed Ramachandran plots for the optimized structures indicated that no misoriented amino acids or unreasonable conformations were present.

In the A441T minimized model the distance of the hydrogen atom of the hydroxyl group from the centroid of the aromatic face of W456 ring is of 2.96 Å, suggesting the possible existence of a hydroxyl-aromatic-ring hydrogen bond of the kind described by Levitt and Perutz [ 31].

The quality of the energy minimized model is then verified using PROCHECK available at PDBSUM [ 64] webserver.

Therefore, in our article, we first obtained energy minimized model structures and only then used MD simulations to tackle the dynamics of some of them.

Third, an optimization algorithm was used to identify the menu design that minimized model predicted search times based on predefined search frequencies of different menu items.

Energy minimized model was subjected to position-restrained MD with NPT ensemble keeping number of particles (N), system pressure (P), and temperature (T) as constant parameters.