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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 ] .
vdWC = van der Waals Clash
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).
The efficient prediction of peptide side-chain conformations in the groove has been shown mainly due to van der Waals contribution.
After careful visual inspection for shape complementarity, hydrogen bonding network, compound flexibility, and potential Van der Waals clashes, 30 molecules out of 300 were selected and purchased to be experimentally tested in vitro . We should stress out here that the Van der Waals term is too noisy to be added to the binding energy function, as discussed in details elsewhere [ 21].