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The graphical user interface program AutoDock Tools (Sanner 1999) was used to prepare the structures for all docking simulations.
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The Central Park Visitor Center at Tavern on the Green — which for 18 months has occupied the building that held the once-glittering landmark restaurant Tavern on the Green — will close on Wednesday afternoon for more than a year for a $9.8-million 9.8-million renovationt will project thatstructure for a newillstaurant tenant, as yet unnamed.
To prepare the structure for docking, we deleted all bound ligands and crystallographic waters and flipped the orientation of residue Asn 294 in the binding site (the sidechain amide nitrogen and oxygen had been assigned incorrectly).
To prepare the structure for docking, the ligand and all water molecules were removed.
"Mother Nature has tried everything in her power to beat us". As the fire continued to march toward the homes, firefighters prepared the structures for an anticipated fiery assault.
The power station collapsed Tuesday afternoon while its workers were preparing the structure for demolition.
For each phenol molecule from our data set, we also prepared the structure of the dissociated form, where the hydrogen is missing from the phenolic OH group.
All of this work is preparatory for the creation of the Debt Collective which is preparing the structure needed take on the larger subject of Wall Street manufactured debt.
We suggest that Arg-228 and Asp-382 participate in interactions at the cytoplasmic side, possibly by attracting the substrate out from the cavity, preparing the structure for the periplasmic-open conformation and a new transport cycle.
Discovery Studio 3.0 (Accelrys Inc., San Diego, CA, USA) to prepare the enzyme structures; alternate conformations were removed and incomplete chains with missing residues and hydrogen atoms were added.
We used PDB2PQR [ 75, 76] to prepare the setup (structures and parameters) for calculations, and APBS [ 77] for modeling properties of protein surfaces by solving the Poisson-Boltzmann equation.
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