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:
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 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).
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].
This binding site coincides with that of AChBP, and is in agreement with photo-affinity labeling and mutagenesis study [ 6 11 ] . The ligand makes Van der Waals contact with Trp182, Tyr230 and Cys225-226 of alpha4, and Trp82, Leu146 and Phe144 of beta2 (Figure 3- Top).
The efficient prediction of peptide side-chain conformations in the groove has been shown mainly due to van der Waals contribution.
Loading...