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Example sentences for: waals

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The scoring functions used for the final filtering include the all-atom function [ 32 ] , hydrophobic compactness [ 40 ] , a simple residue-residue contact function [ 44 ] , a density-scoring function that is based on the distance of a conformation to all its relatives in the conformation pool, contact order [ 45 ] , a secondary structure based scoring function that evaluates the match between the predicted structure and the secondary structure of a final energy-minimised conformation, and standard physics-based electrostatics and Van der Waals terms [ 46 ] .
The flexible ligand was docked into a combination of five potential map representations of the RAR-α ligand binding pocket, which account for two Van der Waals boundaries, hydrophobicity, electrostatics and hydrogen bonding profiles [ 20, 27].
Energy terms included Van der Waals, electrostatic, hydrogen bond, and torsion terms [ 10 ] .
Nicotine makes Van Der Waals contacts with the same array of receptor side-chains (Figure 3- Bottom).
One hundred steps of energy minimization of the protein-ligand-water complex were initially performed, followed by 10 ps MD simulation at 300 K, with an atom-based shifted distance-dependent dielectric constant, ε = 4r; a switch function on van der Waals interaction, and a time step of 1 femtosecond (fs).