Words similar to waals
Example sentences for: waals
How can you use “waals” in a sentence? Here are some example sentences to help you improve your vocabulary:
Of the two additional key terms, the van der Waals component operates with a very short range force and essentially prevents atom-atom interpenetration.
The Van der Waals interaction energies were calculated separately, and are also presented.
The van der Waals, bond, angle, dihedral, and improper dihedral parameters for all the ligands were adopted from the Hetero-compound Information Centre-Uppsala HIC-Up http://xray.bmc.uu.se/hicup [ 55 ] . The water molecule under the flaps present in all complexes was included in all steps throughout this study except for 1hvr, where the structural water was removed in the preparation of the protease to be docked with the ligand (the ligand of 1hvr, which is a urea-based inhibitor, does not bind a water molecule in this position).
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 binding energy function, previously validated against a diversified benchmark [ 20 ] , includes a hydrophobic term, an electrostatic term, and an entropic term, but does not include Van der Waals energy, since this term is too noisy; Van der Waals interactions are supposed to be proportional to the interface of the interacting molecules, and incorporated into the surface (hydrophobic) term (see Materials and Methods).
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